### yaleDavisHarvardSnyder.txt wrangler notes for all submissions
select id,name,status from projects where name like "Y%";
4+-----+------------------------------------+-----------------+
| id | name | status |
+-----+------------------------------------+-----------------+
| 12 | YHD_HeLa-S3_Pol2 | released |
| 13 | YHD_HeLa-S3_IFNg_STAT1 | released |
| 14 | YHD_HeLa-S3_Input | released |
| 15 | YHD_HeLa-S3_IFNg_Input | released |
| 16 | YHD_K562_Pol2 | released |
| 17 | YHD_K562_Input | released |
| 18 | YHD_NB4_Pol2 | released |
| 19 | YHD_NB4_Input | released |
| 68 | YHD_K562_Fos | released |
| 69 | YHD_K562_Myc | released |
| 72 | YHD_K562_Jun | released |
| 91 | YHD_GM12878_Input | released |
| 92 | YHD_GM12878_Pol2 | released |
| 94 | YHD_GM12878_c-Fos | released |
| 107 | YHD Raw Signal Regeneration | released |
| 189 | YHD_K562_NF-E2 | released |
| 190 | YHD_GM12878_Max | released |
| 191 | YHD_HEK293_Input | released |
| 192 | YHD_HEK293_Pol2 | released |
| 193 | YHD_HeLa-S3_Large_Fragment_Control | released |
| 194 | YHD_HeLa-S3_MNase_Control | released |
| 195 | YHD_HeLa-S3_MouseIgG_Control | released |
| 196 | YHD_HeLa-S3_Naked_DNA_Control | released |
| 205 | YHD_K562_ZNF263 | released |
| 224 | YHD_HCT-116_Input | released |
| 225 | YHD_HCT-116_TCF4 | released |
| 226 | YHD_K562_Max | released |
| 227 | YHD_K562_GATA-1 | released |
| 238 | YHD_K562_JunD | released |
| 239 | YHD_GM12878_JunD | released |
| 240 | YHD_HepG2_Input | released |
| 241 | YHD_HepG2_Pol2 | released |
| 242 | YHD_HepG2_SREBP1A | released |
| 243 | YHD_HepG2_SREBP2 | released |
| 276 | YHD_K562_PolyA_RNA | displayed |
| 279 | YHD_Input_WIGs | displayed |
| 315 | YDH_HeLa-S3_c-Fos | validate failed |
| 316 | YDH_HeLa-S3_Myc | validate failed |
| 317 | YDH_HeLa-S3_Max | validate failed |
| 318 | YDH_GM12878_Pol3 | validate failed |
| 319 | YDH_K562_Rad21 | validate failed |
| 320 | YDH_K562_XRCC4 | validate failed |
| 323 | YDH_narrowPeak_updates | loaded |
| 324 | YDH_wiggle_updates | loaded |
+-----+------------------------------------+-----------------+
44 rows in set (0.00 sec)
Yale Round 1
============
/cluster/encodeftp/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/12 > validate_error 2>&1
/cluster/encodeftp/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/13 > validate_error 2>&1
/cluster/encodeftp/bin/doEncodeValidate.pl -quick x /cluster/data/encode/pipeline/encpipeline_prod/14 > validate_error 2>&1
/cluster/encodeftp/bin/doEncodeValidate.pl -quick x /cluster/data/encode/pipeline/encpipeline_prod/15 > /cluster/data/encode/pipeline/encpipeline_prod/15/validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeValidate.pl -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/14 > /cluster/data/encode/pipeline/encpipeline_prod/14/validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeValidate.pl -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/15 > /cluster/data/encode/pipeline/encpipeline_prod/15/validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/12 > validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/13 > validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/14 > upload_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/15 > upload_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/12 > upload_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/13 > upload_error 2>&1 &
Replace
variableStep chrom=chr1 [span=windowSize]
with
variableStep chrom=chr1
mv HeLa-S3_IFNg_Input.wig HeLa-S3_IFNg_Input.wig.bak
cat HeLa-S3_IFNg_Input.wig.bak | sed s/" \[span=windowSize\]$"//g > HeLa-S3_IFNg_Input.wig &
mv HeLa-S3_Input.wig HeLa-S3_Input.wig.bak
cat HeLa-S3_Input.wig.bak | sed s/" \[span=windowSize\]$"//g > HeLa-S3_Input.wig &
mv IFNg_HeLa-S3_STAT1.wig IFNg_HeLa-S3_STAT1.wig.bak
cat IFNg_HeLa-S3_STAT1.wig.bak | sed s/" \[span=windowSize\]$"//g > IFNg_HeLa-S3_STAT1.wig &
mv HeLa-S3_Pol2.wig HeLa-S3_Pol2.wig.bak
cat HeLa-S3_Pol2.wig.bak | sed s/" \[span=windowSize\]$"//g > HeLa-S3_Pol2.wig &
ERROR: failed creation of wiggle for antibody=Input;cell=HeLa-S3_IFNg;1ERROR: chrM 16537 16572
chromEnd > chromSize ? 16572 > 140273252
sort: write failed: -: Broken pipe
sort: write error
Error:
failed creation of wiggle for 'antibody=Input;cell=HeLa-S3_IFNg;1'
sort -k1,1 -k2,2n HeLa-S3_IFNg_Input_tagAlign_rep1_laneE_FC203E3_20080111_s_2.bed | /cluster/home/tdreszer/bin/x86_64/bedItemOverlapCount hg18 stdin tmp.wig &
Yale Round 2
============
1) Failure to submit after ftp
2) Archives do not have DAF and DDF at root mv Yale_K562_Pol2/* .;rmdir Yale_K562_Pol2
3) Ask about the HeLa_S3_Pol2.tar
/cluster/encodeftp/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/16 > /cluster/data/encode/pipeline/encpipeline_prod/16/validate_error 2>&1
/cluster/encodeftp/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/16 > /cluster/data/encode/pipeline/encpipeline_prod/16/validate_error 2>&1 &
Error:
Invalid narrowPeak file; line 1069 in file 'Data/Yale_K562_Pol2_narrowPeak.pk' is invalid:
line: chr4 48789516 48789679 . 0 . 0.35598 3e-05 -1 [validateNarrowPeak]
my $floatRegEx = "[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|))";
my $floatRegEx = "[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|\\e[+-]?d+))";
my $floatRegEx = "[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|[eE]{1}?[+-]{1}?\\d+))";
my $floatRegEx = "[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?";
my $floatRegEx = "[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?";
grep -P "^chr(\d+|M|X|Y)\s+\d+\s+\d+\s+\S+\s+\d+\s+[+-\.]\s+$floatRegEx\s+$floatRegEx\s+[+-]?\d+$"
grep -P "^chr(\d+|M|X|Y)\s+\d+\s+\d+\s+\S+\s+\d+\s+[+-\.]\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s+[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s+[+-]?\d+$" tmp.pk | wc -l
grep -P "^chr(\d+|M|X|Y)\s+\d+\s+\d+\s+\S+\s+\d+\s+[+-\.]\s+[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|))\s+[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|))\s+[+-]?\d+$" tmp.pk
grep -P "^chr(\d+|M|X|Y)\s+\d+\s+\d+\s+\S+\s+\d+\s+[+-\.]\s+[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|\\e[+-]?d+))\s+[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|\\e[+-]?d+))\s+[+-]?\d+$" tmp.pk
grep -P "^chr(\d+|M|X|Y)\s+\d+\s+\d+\s+\S+\s+\d+\s+[+-\.]\s+[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|\\e[+-]?d+))\s+[+-]?(?:\\.\\d+|\\d+(?:\\.\\d+|\\e{1}[+-]{1}d+))\s+[+-]?\d+$" tmp.pk
grep -P "^chr(\d+|M|X|Y)\s+\d+\s+\d+\s+\S+\s+\d+\s+[+-\.]\s+[+-]?(?:\.\d+|\d+(?:\.\d+|e[+-]?\d+))\s+[+-]?(?:\.\d+|\d+(?:\.\d+|[eE]{1}?[+-]{1}?\d+))\s+[+-]?\d+$" tmp.pk
/cluster/encodeftp/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/16 > /cluster/data/encode/pipeline/encpipeline_prod/16/validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/16 > /cluster/data/encode/pipeline/encpipeline_prod/16/upload_error 2>&1 &
update wgEncodeYaleChIPseqPeaksK562Pol2 set chromStart = chromStart - 1;
/cluster/encodeftp/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/17 > /cluster/data/encode/pipeline/encpipeline_prod/17/validate_error 2>&1
Error(s):
File 'Data/Yale_K562_Pol2_tagAlign_rep1*.bed' does not exist (possibly bad glob?)
Antibody '' is not known
Antibody '' is not known
Antibody '' is not known
e Yale_K562_input.DDF
/cluster/encodeftp/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/17 > /cluster/data/encode/pipeline/encpipeline_prod/17/validate_error 2>&1
/cluster/encodeftp/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/17 > /cluster/data/encode/pipeline/encpipeline_prod/17/validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/17 > /cluster/data/encode/pipeline/encpipeline_prod/17/upload_error 2>&1 &
insert into project_files set file_name = "YaleChipSeq.DAF", file_size = 1013,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Yale_K562_Pol2.DDF", file_size = 429,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2.wig", file_size = 342929765,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_narrowPeak.pk", file_size = 3774328,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_sequence_rep1_laneA_FC20GEBA_062708_s_5.fastq",file_size = 612714082,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_sequence_rep1_laneB_FC20GEBA_062708_s_6.fastq",file_size = 596455168,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_sequence_rep2_laneA_FC20GEBA_062708_s_7.fastq",file_size = 636639150,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_sequence_rep2_laneB_FC20GEBA_062708_s_8.fastq",file_size = 611535870,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_tagAlign_rep1_laneA_FC20GEBA_062708_s_5.bed", file_size = 276323791,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_tagAlign_rep1_laneB_FC20GEBA_062708_s_6.bed", file_size = 265073044,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_tagAlign_rep2_laneA_FC20GEBA_062708_s_7.bed", file_size = 263266653,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Pol2_tagAlign_rep2_laneB_FC20GEBA_062708_s_8.bed", file_size = 254118963,file_date = now(),project_archive_id = 59,created_at = now(),updated_at = now();
insert into project_files set file_name = "YaleChipSeqInput.DAF",file_size = 875,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Yale_K562_Input.DDF",file_size = 244,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input.wig",file_size = 283131730,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_sequence_rep1_laneA_FC2039PAA_021408_s_1.fastq",file_size = 191801940,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_sequence_rep1_laneB_FC200NVAA_041408_s_8.fastq",file_size = 410332396,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_sequence_rep1_laneC_FC20698AA_031908_s_1.fastq",file_size = 263611046,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_sequence_rep1_laneD_FC20H9NAA_061008_s_2.fastq",file_size = 194980106,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_sequence_rep1_laneE_FC20H9NAA_061008_s_3.fastq",file_size = 196893350,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_tagAlign_rep1_laneA_FC2039PAA_021408_s_1.bed",file_size = 65429709,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_tagAlign_rep1_laneB_FC200NVAA_041408_s_8.bed",file_size = 165782646,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_tagAlign_rep1_laneC_FC20698AA_031908_s_1.bed",file_size = 104562141,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_tagAlign_rep1_laneD_FC20H9NAA_061008_s_2.bed",file_size = 224111258,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_K562_Input_tagAlign_rep1_laneE_FC20H9NAA_061008_s_3.bed",file_size = 234640662,file_date = now(),project_archive_id = 60,created_at = now(),updated_at = now();
insert into project_files set file_name = "YaleChipSeq.DAF",file_size = 1013,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Yale_NB4_Pol2.DDF",file_size = 540,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2.wig",file_size = 336599917,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_narrowPeak.pk",file_size = 3178313,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep1_laneA_FC12037_112207_s_3.fastq",file_size = 189903090,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep1_laneB_071115_HWI-EAS134_0011_s_1.fastq",file_size = 507888122,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep1_laneC_FC12482_110107_s_4.fastq",file_size = 141047434,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep2_laneA_071115_HWI-EAS134_0011_s_2.fastq",file_size = 447962946,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep2_laneB_FC12169_111107_s_4.fastq",file_size = 271109612,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep3_laneA_071115_HWI-EAS134_0011_s_3.fastq",file_size = 463097958,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_sequence_rep3_laneB_FC12169_111107_s_8.fastq",file_size = 117151474,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep1_laneA_FC12037_112207_s_3.bed",file_size = 192233406,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep1_laneB_071115_HWI-EAS134_0011_s_1.bed",file_size = 313383903,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep1_laneC_FC12482_110107_s_4.bed",file_size = 74941124,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep2_laneA_071115_HWI-EAS134_0011_s_2.bed",file_size = 239090463,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep2_laneB_FC12169_111107_s_4.bed",file_size = 124332313,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep3_laneA_071115_HWI-EAS134_0011_s_3.bed",file_size = 234465450,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Pol2_tagAlign_rep3_laneB_FC12169_111107_s_8.bed",file_size = 49711922,file_date = now(),project_archive_id = 61,created_at = now(),updated_at = now();
insert into project_files set file_name = "YaleChipSeqInput.DAF",file_size = 875,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Yale_NB4_Input.DDF",file_size = 238,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input.wig",file_size = 201104739,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_sequence_rep1_laneA_FC202KCAA_121407_s_4.fastq",file_size = 489758874,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_sequence_rep1_laneB_FC202KCAA_121407_s_5.fastq",file_size = 480799786,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_sequence_rep1_laneC_FC203FWAA_010508_s_5.fastq",file_size = 254244316,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_sequence_rep1_laneD_FC203FWAA_010508_s_6.fastq",file_size = 528650320,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_tagAlign_rep1_laneA_FC202KCAA_121407_s_4.bed",file_size = 137832575,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_tagAlign_rep1_laneB_FC202KCAA_121407_s_5.bed",file_size = 128765746,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_tagAlign_rep1_laneC_FC203FWAA_010508_s_5.bed",file_size = 97146008,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
insert into project_files set file_name = "Data/Yale_NB4_Input_tagAlign_rep1_laneD_FC203FWAA_010508_s_6.bed",file_size = 222055868,file_date = now(),project_archive_id = 62,created_at = now(),updated_at = now();
doEncodeValidate.pl -allowReloads -skipValidateFiles -skipAutoCreation -skipOutput x 16
### Fix narrowPeak to be 3 slot:
head Yale_K562_Pol2_narrowPeak.pk
chr4 30984 31010 . 0 . 8.77251 2.92998 -1
chr4 38025 38043 . 0 . 1.16966 0.36879 -1
cp Yale_K562_Pol2_narrowPeak.pk Yale_K562_Pol2_narrowPeak_2Slot.pk
/cse/staff/tdreszer/docs/ENCODE/convertTo3Slot.sh -p Yale_K562_Pol2_narrowPeak_2Slot.pk Yale_K562_Pol2_narrowPeak.pk
/cluster/encodeftp/bin/doEncodeValidate.pl x -allowReloads /cluster/data/encode/pipeline/encpipeline_prod/16 > /cluster/data/encode/pipeline/encpipeline_prod/16/validate_error 2>&1 &
/cluster/encodeftp/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/16 > /cluster/data/encode/pipeline/encpipeline_prod/16/upload_error 2>&1 &
# make a new tar for NCBI
tar -cpzf YaleK562Pol2.tgz YaleChipSeq.DAF Yale_K562_Pol2_corrected.DDF Data &
# test v1.0 DAF
/cluster/encodeftp/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/16 > test_error 2>&1
# passed
# Converting tests to 3 slot
/cse/staff/tdreszer/docs/ENCODE/convertTo3Slot.sh SL_167_peak_caller.ChIP.peaks SL_167_peak_caller.ChIP.pks
/cse/staff/tdreszer/docs/ENCODE/convertTo3Slot.sh -p Yale_NB4_Pol2_narrowPeak_2Slot.pk Yale_NB4_Pol2_narrowPeak.pk
awk '{printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t-1\t%s\t%s\n",$1,$2,$3,$4,$5,$6,$7,$9,$10;}' Yale_K562_Pol2_narrowPeak.pk > Data/Yale_K562_Pol2_narrowPeak-1.pk
/cluster/home/tdreszer/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/16 > test_error 2>&1
Yale 11-20
==========
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/72 > validate_error 2>&1
1) Unregistered antibodies
2) Invalid narrowPeak file; line 1 in file 'Data/Yale_K562_Jun_narrowPeak.pk' is invalid;
not enough fields;
line: chr1 555270 555865 . 0 . 0.76651 0.02235 -1 [validateNarrowPeak]
# Converting Peaks to 3 slot
mv Yale_K562_Jun_narrowPeak.pk Yale_K562_Jun_narrowPeak_2Slot.pk
/cse/staff/tdreszer/docs/ENCODE/convertTo3Slot.sh -q Yale_K562_Jun_narrowPeak_2Slot.pk Yale_K562_Jun_narrowPeak.pk
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/72 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/72 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/72 > upload_error 2>&1 &
cd 68;mv ../../ftp/prod/mpw6/Yale_K562_Fos.tgz .
tar -xzf Yale_K562_Fos.tgz &
mv Yale_K562_Fos.tgz 001_Yale_K562_Fos.tgz
mv Yale_K562_Fos/* .
rmdir Yale_K562_Fos
cd Data
mv Yale_K562_Fos_narrowPeak.pk Yale_K562_Fos_narrowPeak_2Slot.pk
/cse/staff/tdreszer/docs/ENCODE/convertTo3Slot.sh -q Yale_K562_Fos_narrowPeak_2Slot.pk Yale_K562_Fos_narrowPeak.pk
cd ..
e Yale_K562_Fos.DF Fos -> c-Fos space -> tab
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/68 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/68 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/68 > upload_error 2>&1 &
cd 69;mv ../../ftp/prod/mpw6/Yale_K562_Myc.tgz .
tar -xzf Yale_K562_Myc.tgz &
mv Yale_K562_Myc.tgz 001_Yale_K562_Myc.tgz
mv Yale_K562_Myc/* .
rmdir Yale_K562_Myc
cd Data
mv Yale_K562_Myc_narrowPeak.pk Yale_K562_Myc_narrowPeak_2Slot.pk
/cse/staff/tdreszer/docs/ENCODE/convertTo3Slot.sh -q Yale_K562_Myc_narrowPeak_2Slot.pk Yale_K562_Myc_narrowPeak.pk
cd ..
e Yale_K562_Myc.DF Myc -> c-Myc space -> tab
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/69 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/69 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/69 > upload_error 2>&1 &
Yale 11-25 NB4 at last
======================
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/18 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/18 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/18 > upload_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/19 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/19 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/19 > upload_error 2>&1 &
Yale 11-26
==========
Remove *_random chrs
grep -v "_random" old/*.bed | grep -v "_hap" > *.bed
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/92 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/92 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/92 > upload_error 2>&1 &
medianFragmentLength
====================
| 94 | Yale_GM12878_c-Fos | displayed |
| 91 | Yale_GM12878_Input | displayed |
| 92 | Yale_GM12878_Pol2 | displayed |
| 15 | Yale_HeLa-S3_IFNg_Input | displayed |
| 13 | Yale_HeLa-S3_IFNg_STAT1 | displayed |
| 14 | Yale_HeLa-S3_Input | displayed |
| 12 | Yale_HeLa-S3_Pol2 | displayed |
| 68 | Yale_K562_Fos | displayed |
| 17 | Yale_K562_Input | displayed |
| 72 | Yale_K562_Jun | displayed |
| 69 | Yale_K562_Myc | displayed |
| 16 | Yale_K562_Pol2 | displayed |
| 19 | Yale_NB4_Input | displayed |
| 18 | Yale_NB4_Pol2 | displayed |
grep Alignment 92/*.DDF
94/Data/Yale_GM12878_c-Fos_tagAlign_rep1_FC20GEE_062208_s_1.bed Alignments GM12878 c-Fos 1
94/Data/Yale_GM12878_c-Fos_tagAlign_rep2_FC20GEE_062208_s_2.bed Alignments GM12878 c-Fos 2
94/Data/Yale_GM12878_c-Fos_tagAlign_rep3_FC20GEE_062208_s_3.bed Alignments GM12878 c-Fos 3
92/Data/Yale_GM12878_Pol2_tagAlign_rep1_laneA_FC201BPAA_032708_s_7.bed Alignments GM12878 Pol2 1
92/Data/Yale_GM12878_Pol2_tagAlign_rep1_laneB_FC201BPAA_032708_s_8.bed Alignments GM12878 Pol2 1
92/Data/Yale_GM12878_Pol2_tagAlign_rep2_laneA_FC20698AA_031908_s_5.bed Alignments GM12878 Pol2 2
92/Data/Yale_GM12878_Pol2_tagAlign_rep2_laneB_FC20698AA_031908_s_6.bed Alignments GM12878 Pol2 2
13/IFNg_HeLa-S3_STAT1_tagAlign_rep1_lane*.bed Alignments HeLa-S3_IFNg STAT1 1 GSE12782
13/IFNg_HeLa-S3_STAT1_tagAlign_rep2_lane*.bed Alignments HeLa-S3_IFNg STAT1 2 GSE12782
12/HeLa-S3_Pol2_tagAlign_rep1_lane*.bed Alignments HeLa-S3 Pol2 1 GSE12781
12/HeLa-S3_Pol2_tagAlign_rep2_lane*.bed Alignments HeLa-S3 Pol2 2 GSE12781
12/HeLa-S3_Pol2_tagAlign_rep3_lane*.bed Alignments HeLa-S3 Pol2 3 GSE12781
68/Data/Yale_K562_Fos_tagAlign_rep1_FC20GEE_062208_s_4.bed Alignments K562 c-Fos 1
68/Data/Yale_K562_Fos_tagAlign_rep2_FC20GEE_062208_s_5.bed Alignments K562 c-Fos 2
68/Data/Yale_K562_Fos_tagAlign_rep3_FC20GEE_062208_s_6.bed Alignments K562 c-Fos 3
72/Data/Yale_K562_Jun_tagAlign_rep1*.bed Alignments K562 c-Jun 1
72/Data/Yale_K562_Jun_tagAlign_rep2*.bed Alignments K562 c-Jun 2
69/Data/Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7.bed Alignments K562 c-Myc 1
69/Data/Yale_K562_Myc_tagAlign_rep2_FC20GEE_062208_s_8.bed Alignments K562 c-Myc 2
16/Data/Yale_K562_Pol2_tagAlign_rep1*.bed Alignments K562 Pol2 1
16/Data/Yale_K562_Pol2_tagAlign_rep2*.bed Alignments K562 Pol2 2
18/Data/Yale_NB4_Pol2_tagAlign_rep1*.bed Alignments NB4 Pol2 1
18/Data/Yale_NB4_Pol2_tagAlign_rep2*.bed Alignments NB4 Pol2 2
18/Data/Yale_NB4_Pol2_tagAlign_rep3*.bed Alignments NB4 Pol2 3
91/Data/Yale_GM12878_Input_tagAlign_FC200NVAA_041408_s_7.bed Alignments GM12878 Input 1
91/Data/Yale_GM12878_Input_tagAlign_FC20H9WAA_061208_s_6.bed Alignments GM12878 Input 1
91/Data/Yale_GM12878_Input_tagAlign_FC20H9WAA_061208_s_7.bed Alignments GM12878 Input 1
91/Data/Yale_GM12878_Input_tagAlign_FC20H9WAA_061208_s_8.bed Alignments GM12878 Input 1
15/HeLa-S3_IFNg_Input_tagAlign_rep1_lane*.bed Alignments HeLa-S3_IFNg Input 1 GSE12782
14/HeLa-S3_Input_DNA_tagAlign_rep1_lane*.bed Alignments HeLa-S3 Input 1 GSE12781
17/Data/Yale_K562_Input_tagAlign_rep1*.bed Alignments K562 Input 1
19/Data/Yale_NB4_Input_tagAlign_rep1*.bed Alignments NB4 Input 1
mkdir Data
cp ../94/Data/Yale_GM12878_c-Fos_tagAlign_rep1_FC20GEE_062208_s_1.bed Data/
cp ../94/Data/Yale_GM12878_c-Fos_tagAlign_rep2_FC20GEE_062208_s_2.bed Data/
cp ../94/Data/Yale_GM12878_c-Fos_tagAlign_rep3_FC20GEE_062208_s_3.bed Data/
cp ../92/Data/Yale_GM12878_Pol2_tagAlign_rep1_laneA_FC201BPAA_032708_s_7.bed Data/
cp ../92/Data/Yale_GM12878_Pol2_tagAlign_rep1_laneB_FC201BPAA_032708_s_8.bed Data/
cp ../92/Data/Yale_GM12878_Pol2_tagAlign_rep2_laneA_FC20698AA_031908_s_5.bed Data/
cp ../92/Data/Yale_GM12878_Pol2_tagAlign_rep2_laneB_FC20698AA_031908_s_6.bed Data/
cp ../13/IFNg_HeLa-S3_STAT1_tagAlign_rep1_lane*.bed Data/
cp ../13/IFNg_HeLa-S3_STAT1_tagAlign_rep2_lane*.bed Data/
cp ../12/HeLa-S3_Pol2_tagAlign_rep1_lane*.bed Data/
cp ../12/HeLa-S3_Pol2_tagAlign_rep2_lane*.bed Data/
cp ../12/HeLa-S3_Pol2_tagAlign_rep3_lane*.bed Data/
cp ../68/Data/Yale_K562_Fos_tagAlign_rep1_FC20GEE_062208_s_4.bed Data/
cp ../68/Data/Yale_K562_Fos_tagAlign_rep2_FC20GEE_062208_s_5.bed Data/
cp ../68/Data/Yale_K562_Fos_tagAlign_rep3_FC20GEE_062208_s_6.bed Data/
cp ../72/Data/Yale_K562_Jun_tagAlign_rep1*.bed Data/
cp ../72/Data/Yale_K562_Jun_tagAlign_rep2*.bed Data/
cp ../69/Data/Yale_K562_Myc_tagAlign_rep1_FC20GEE_062208_s_7.bed Data/
cp ../69/Data/Yale_K562_Myc_tagAlign_rep2_FC20GEE_062208_s_8.bed Data/
cp ../16/Data/Yale_K562_Pol2_tagAlign_rep1*.bed Data/
cp ../16/Data/Yale_K562_Pol2_tagAlign_rep2*.bed Data/
cp ../18/Data/Yale_NB4_Pol2_tagAlign_rep1*.bed Data/
cp ../18/Data/Yale_NB4_Pol2_tagAlign_rep2*.bed Data/
cp ../18/Data/Yale_NB4_Pol2_tagAlign_rep3*.bed Data/
mkdir Inputs
cp ../91/Data/Yale_GM12878_Input_tagAlign_FC200NVAA_041408_s_7.bed Inputs/
cp ../91/Data/Yale_GM12878_Input_tagAlign_FC20H9WAA_061208_s_6.bed Inputs/
cp ../91/Data/Yale_GM12878_Input_tagAlign_FC20H9WAA_061208_s_7.bed Inputs/
cp ../91/Data/Yale_GM12878_Input_tagAlign_FC20H9WAA_061208_s_8.bed Inputs/
cp ../15/HeLa-S3_IFNg_Input_tagAlign_rep1_lane*.bed Inputs/
cp ../14/HeLa-S3_Input_DNA_tagAlign_rep1_lane*.bed Inputs/
cp ../17/Data/Yale_K562_Input_tagAlign_rep1*.bed Inputs/
cp ../19/Data/Yale_NB4_Input_tagAlign_rep1*.bed Inputs/
edit YaleChipSeqRegen.DAF .DDF
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/107 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/107 > upload_error 2>&1 &
edit YaleChipSeqRegenInputs.DAF .DDF
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/107 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/107 > upload_error 2>&1 &
| 94 | Yale_GM12878_c-Fos | displayed |
| 92 | Yale_GM12878_Pol2 | displayed |
| 13 | Yale_HeLa-S3_IFNg_STAT1 | displayed |
| 12 | Yale_HeLa-S3_Pol2 | displayed |
| 68 | Yale_K562_Fos | displayed |
| 72 | Yale_K562_Jun | displayed |
| 69 | Yale_K562_Myc | displayed |
| 16 | Yale_K562_Pol2 | displayed |
| 18 | Yale_NB4_Pol2 | displayed |
cd 94
/bin/gzip -c Data/Yale_GM12878_c-Fos_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Cfos.narrowPeak.gz &
cd 92
/bin/gzip -c Data/Yale_GM12878_Pol2_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2.narrowPeak.gz &
cd 12
/bin/gzip -c Yale_HeLa-S3_Pol2_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3Pol2.narrowPeak.gz &
cd 13
/bin/gzip -c Yale_HeLa-S3-IFNg_STAT1_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz &
cd 68
/bin/gzip -c Data/Yale_K562_Fos_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Cfos.narrowPeak.gz &
cd 72
/bin/gzip -c Data/Yale_K562_Jun_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Cjun.narrowPeak.gz &
cd 69
/bin/gzip -c Data/Yale_K562_Myc_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Cmyc.narrowPeak.gz &
cd 16
/bin/gzip -c Data/Yale_K562_Pol2_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Pol2.narrowPeak.gz &
cd 18
/bin/gzip -c Data/Yale_NB4_Pol2_narrowPeak.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksNb4Pol2.narrowPeak.gz &
Yale PushQ
==========
=================
wgEncodeYaleChIPseqPeaksGm12878Cfos\n
wgEncodeYaleChIPseqPeaksGm12878Pol2\n
wgEncodeYaleChIPseqPeaksHelas3Pol2\n
wgEncodeYaleChIPseqPeaksHelas3ifngStat1\n
wgEncodeYaleChIPseqPeaksK562Cfos\n
wgEncodeYaleChIPseqPeaksK562Cjun\n
wgEncodeYaleChIPseqPeaksK562Cmyc\n
wgEncodeYaleChIPseqPeaksK562Pol2\n
wgEncodeYaleChIPseqPeaksNb4Pol2\n
wgEncodeYaleChIPseqRawSignalGm12878Input\n
wgEncodeYaleChIPseqRawSignalHelas3Input\n
wgEncodeYaleChIPseqRawSignalHelas3ifngInput\n
wgEncodeYaleChIPseqRawSignalK562Input\n
wgEncodeYaleChIPseqRawSignalNb4Input\n
wgEncodeYaleChIPseqRawSignalRep1Gm12878Cfos\n
wgEncodeYaleChIPseqRawSignalRep1Gm12878Pol2\n
wgEncodeYaleChIPseqRawSignalRep1Helas3Pol2\n
wgEncodeYaleChIPseqRawSignalRep1Helas3ifngStat1\n
wgEncodeYaleChIPseqRawSignalRep1K562Cfos\n
wgEncodeYaleChIPseqRawSignalRep1K562Cjun\n
wgEncodeYaleChIPseqRawSignalRep1K562Cmyc\n
wgEncodeYaleChIPseqRawSignalRep1K562Pol2\n
wgEncodeYaleChIPseqRawSignalRep1Nb4Pol2\n
wgEncodeYaleChIPseqRawSignalRep2Gm12878Cfos\n
wgEncodeYaleChIPseqRawSignalRep2Gm12878Pol2\n
wgEncodeYaleChIPseqRawSignalRep2Helas3Pol2\n
wgEncodeYaleChIPseqRawSignalRep2Helas3ifngStat1\n
wgEncodeYaleChIPseqRawSignalRep2K562Cfos\n
wgEncodeYaleChIPseqRawSignalRep2K562Cjun\n
wgEncodeYaleChIPseqRawSignalRep2K562Cmyc\n
wgEncodeYaleChIPseqRawSignalRep2K562Pol2\n
wgEncodeYaleChIPseqRawSignalRep2Nb4Pol2\n
wgEncodeYaleChIPseqRawSignalRep3Gm12878Cfos\n
wgEncodeYaleChIPseqRawSignalRep3Helas3Pol2\n
wgEncodeYaleChIPseqRawSignalRep3K562Cfos\n
wgEncodeYaleChIPseqRawSignalRep3Nb4Pol2\n
wgEncodeYaleChIPseqSignalGm12878Cfos\n
wgEncodeYaleChIPseqSignalGm12878Input\n
wgEncodeYaleChIPseqSignalGm12878Pol2\n
wgEncodeYaleChIPseqSignalHelas3Input\n
wgEncodeYaleChIPseqSignalHelas3Pol2\n
wgEncodeYaleChIPseqSignalHelas3ifngInput\n
wgEncodeYaleChIPseqSignalHelas3ifngStat1\n
wgEncodeYaleChIPseqSignalK562Cfos\n
wgEncodeYaleChIPseqSignalK562Cjun\n
wgEncodeYaleChIPseqSignalK562Cmyc\n
wgEncodeYaleChIPseqSignalK562Input\n
wgEncodeYaleChIPseqSignalK562Pol2\n
wgEncodeYaleChIPseqSignalNb4Input\n
wgEncodeYaleChIPseqSignalNb4Pol2\n
wgEncodeYaleChipSeqPol2HelaSites\n
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsHelas3Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsHelas3ifngInput.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsK562Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsNb4Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cfos.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1Helas3Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1Helas3ifngStat1.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1K562Cfos.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1K562Cjun.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1K562Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep1Nb4Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cfos.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2Helas3Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2Helas3ifngStat1.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2K562Cfos.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2K562Cjun.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2K562Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2K562Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep2Nb4Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep3Gm12878Cfos.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep3Helas3Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep3K562Cfos.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqAlignmentsRep3Nb4Pol2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Cfos.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3Pol2.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Cfos.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Cjun.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Cmyc.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562Pol2.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksNb4Pol2.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataHelas3Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataHelas3ifngInput.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataK562Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataNb4Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Gm12878Cfos.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Gm12878Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3ifngStat1.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1K562Cfos.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1K562Cjun.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1K562Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1K562Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Nb4Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Gm12878Cfos.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Gm12878Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3ifngStat1.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2K562Cfos.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2K562Cjun.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2K562Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2K562Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Nb4Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Gm12878Cfos.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Helas3Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3K562Cfos.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Nb4Pol2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalGm12878Cfos.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalGm12878Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalGm12878Pol2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalHelas3Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalHelas3Pol2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalHelas3ifngInput.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalHelas3ifngStat1.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalK562Cfos.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalK562Cjun.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalK562Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalK562Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalK562Pol2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalNb4Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqSignalNb4Pol2.wig.gz
/cluster/data/encode/pipeline/encpipeline_prod/12/wgEncodeYaleChIPseqRawSignalRep1Helas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/12/wgEncodeYaleChIPseqRawSignalRep3Helas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/12/wgEncodeYaleChIPseqRawSignalRep2Helas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/12/wgEncodeYaleChIPseqSignalHelas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/13/wgEncodeYaleChIPseqRawSignalRep1Helas3ifngStat1.wib
/cluster/data/encode/pipeline/encpipeline_prod/13/wgEncodeYaleChIPseqSignalHelas3ifngStat1.wib
/cluster/data/encode/pipeline/encpipeline_prod/13/wgEncodeYaleChIPseqRawSignalRep2Helas3ifngStat1.wib
/cluster/data/encode/pipeline/encpipeline_prod/14/wgEncodeYaleChIPseqRawSignalHelas3Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/14/wgEncodeYaleChIPseqSignalHelas3Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/15/wgEncodeYaleChIPseqRawSignalHelas3ifngInput.wib
/cluster/data/encode/pipeline/encpipeline_prod/15/wgEncodeYaleChIPseqSignalHelas3ifngInput.wib
/cluster/data/encode/pipeline/encpipeline_prod/16/wgEncodeYaleChIPseqRawSignalRep1K562Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/16/wgEncodeYaleChIPseqSignalK562Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/16/wgEncodeYaleChIPseqRawSignalRep2K562Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/17/wgEncodeYaleChIPseqRawSignalK562Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/17/wgEncodeYaleChIPseqSignalK562Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/18/wgEncodeYaleChIPseqRawSignalRep1Nb4Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/18/wgEncodeYaleChIPseqRawSignalRep3Nb4Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/18/wgEncodeYaleChIPseqRawSignalRep2Nb4Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/18/wgEncodeYaleChIPseqSignalNb4Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/19/wgEncodeYaleChIPseqRawSignalNb4Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/19/wgEncodeYaleChIPseqSignalNb4Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/68/wgEncodeYaleChIPseqRawSignalRep1K562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/68/wgEncodeYaleChIPseqRawSignalRep3K562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/68/wgEncodeYaleChIPseqRawSignalRep2K562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/68/wgEncodeYaleChIPseqSignalK562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/69/wgEncodeYaleChIPseqRawSignalRep1K562Cmyc.wib
/cluster/data/encode/pipeline/encpipeline_prod/69/wgEncodeYaleChIPseqSignalK562Cmyc.wib
/cluster/data/encode/pipeline/encpipeline_prod/69/wgEncodeYaleChIPseqRawSignalRep2K562Cmyc.wib
/cluster/data/encode/pipeline/encpipeline_prod/72/wgEncodeYaleChIPseqRawSignalRep1K562Cjun.wib
/cluster/data/encode/pipeline/encpipeline_prod/72/wgEncodeYaleChIPseqSignalK562Cjun.wib
/cluster/data/encode/pipeline/encpipeline_prod/72/wgEncodeYaleChIPseqRawSignalRep2K562Cjun.wib
/cluster/data/encode/pipeline/encpipeline_prod/92/wgEncodeYaleChIPseqRawSignalRep1Gm12878Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/92/wgEncodeYaleChIPseqSignalGm12878Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/92/wgEncodeYaleChIPseqRawSignalRep2Gm12878Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalGm12878Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalHelas3Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalHelas3ifngInput.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalK562Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalNb4Input.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1Gm12878Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1Gm12878Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1Helas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1Helas3ifngStat1.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1K562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1K562Cjun.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1K562Cmyc.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1K562Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep1Nb4Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2Gm12878Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2Gm12878Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2Helas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2Helas3ifngStat1.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2K562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2K562Cjun.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2K562Cmyc.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2K562Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep2Nb4Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep3Gm12878Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep3Helas3Pol2.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep3K562Cfos.wib
/cluster/data/encode/pipeline/encpipeline_prod/107/wgEncodeYaleChIPseqRawSignalRep3Nb4Pol2.wib
Yale 1-15-2009
==============
Problem with Alignment replicates on MNase and NakedDNA
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/194 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/196 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/194 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/194 > upload_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/196 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/196 > upload_error 2>&1 &
rm /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataHelas3Mnase.fastq.gz
/bin/cat Data/Yale_HeLa-S3_MNase_sequence_rep1_laneA_FC305KG_20080624_s_1.fastq > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Mnase.fastq
/bin/cat Data/Yale_HeLa-S3_MNase_sequence_rep1_laneB_FC305NC_20080703_s_1.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Mnase.fastq
/bin/cat Data/Yale_HeLa-S3_MNase_sequence_rep2_laneA_FC305NC_20080703_s_8.fastq > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Mnase.fastq
/bin/cat Data/Yale_HeLa-S3_MNase_sequence_rep2_laneB_FC3082F_20080709_s_8.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Mnase.fastq
/bin/gzip /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Mnase.fastq
/bin/gzip /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Mnase.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep1_laneA_FC200TE_20080210_s_1.fastq > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep1_laneB_FC200TE_20080210_s_2.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep1_laneC_FC2044Y_20080216_s_6.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep1_laneD_FC200RR_20080220_s_5.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep2_laneA_FC203A3_20080225_s_3.fastq > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep2_laneB_FC203A3_20080225_s_4.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep2_laneC_FC203A3_20080225_s_5.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep3_laneA_FC203A3_20080225_s_6.fastq > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep3_laneB_FC203A3_20080225_s_7.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Helas3Nakeddna.fastq
/bin/cat Data/Yale_HeLa-S3_Naked_DNA_sequence_rep3_laneC_FC203A3_20080225_s_8.fastq >> /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Helas3Nakeddna.fastq
/bin/gzip /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep1Helas3Nakeddna.fastq
/bin/gzip /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep2Helas3Nakeddna.fastq
/bin/gzip /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep3Helas3Nakeddna.fastq
../../bin/encodeStatus.pl 189 displayed
../../bin/encodeStatus.pl 190 displayed
../../bin/encodeStatus.pl 191 displayed
../../bin/encodeStatus.pl 192 displayed
../../bin/encodeStatus.pl 193 displayed
../../bin/encodeStatus.pl 194 displayed
../../bin/encodeStatus.pl 195 displayed
../../bin/encodeStatus.pl 196 displayed
insert into project_status_logs set project_id = 189, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 190, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 191, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 192, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 193, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 194, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 195, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 196, status = "displayed", created_at = now(), who = "tdreszer";
insert into project_status_logs set project_id = 12, status = "displayed", created_at = "2008-09-26", who = "tdreszer"; | Yale_HeLa-S3_Pol2 | displayed |
insert into project_status_logs set project_id = 13, status = "displayed", created_at = "2008-09-26", who = "tdreszer"; | Yale_HeLa-S3_IFNg_STAT1 | displayed |
insert into project_status_logs set project_id = 14, status = "displayed", created_at = "2008-09-26", who = "tdreszer"; | Yale_HeLa-S3_Input | displayed |
insert into project_status_logs set project_id = 15, status = "displayed", created_at = "2008-09-26", who = "tdreszer"; | Yale_HeLa-S3_IFNg_Input | displayed |
insert into project_status_logs set project_id = 16, status = "displayed", created_at = "2008-10-28", who = "tdreszer"; | Yale_K562_Pol2 | displayed |
insert into project_status_logs set project_id = 17, status = "displayed", created_at = "2008-09-30", who = "tdreszer"; | Yale_K562_Input | displayed |
insert into project_status_logs set project_id = 18, status = "displayed", created_at = "2008-10-15", who = "tdreszer"; | Yale_NB4_Pol2 | displayed |
insert into project_status_logs set project_id = 19, status = "displayed", created_at = "2008-09-30", who = "tdreszer"; | Yale_NB4_Input | displayed |
insert into project_status_logs set project_id = 68, status = "displayed", created_at = "2008-11-22", who = "tdreszer"; | Yale_K562_Fos | displayed |
insert into project_status_logs set project_id = 69, status = "displayed", created_at = "2008-11-22", who = "tdreszer"; | Yale_K562_Myc | displayed |
insert into project_status_logs set project_id = 72, status = "displayed", created_at = "2008-11-22", who = "tdreszer"; | Yale_K562_Jun | displayed |
insert into project_status_logs set project_id = 91, status = "displayed", created_at = "2008-12-01", who = "tdreszer";
insert into project_status_logs set project_id = 92, status = "displayed", created_at = "2008-11-24", who = "tdreszer";
insert into project_status_logs set project_id = 94, status = "displayed", created_at = "2008-12-01", who = "tdreszer";
insert into project_status_logs set project_id = 107,status = "displayed", created_at = "2008-12-02", who = "tdreszer";
insert into project_status_logs set project_id = 31 ,status = "displayed", created_at = "2008-11-07", who = "tdreszer";
insert into project_status_logs set project_id = 79 ,status = "displayed", created_at = "2008-11-21", who = "tdreszer";
insert into project_status_logs set project_id = 104,status = "displayed", created_at = "2008-12-02", who = "tdreszer";
insert into project_status_logs set project_id = 112,status = "displayed", created_at = "2008-12-06", who = "tdreszer";
insert into project_status_logs set project_id = 114,status = "displayed", created_at = "2008-12-08", who = "tdreszer";
insert into project_status_logs set project_id = 116,status = "displayed", created_at = "2008-12-08", who = "tdreszer";
insert into project_status_logs set project_id = 127,status = "displayed", created_at = "2008-12-10", who = "tdreszer";
insert into project_status_logs set project_id = 131,status = "displayed", created_at = "2008-12-11", who = "tdreszer";
insert into project_status_logs set project_id = 140,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 141,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 142,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 143,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 144,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 145,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 146,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 147,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 148,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 149,status = "displayed", created_at = "2009-01-05", who = "tdreszer";
insert into project_status_logs set project_id = 162,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 163,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 164,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 165,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 166,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 167,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 168,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 169,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 170,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 171,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 172,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 173,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 150,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 151,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 152,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 153,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 154,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 155,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 156,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 157,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 158,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 159,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 160,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 161,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 66,status = "displayed", created_at = "2008-12-05", who = "tdreszer";
insert into project_status_logs set project_id = 108,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 174,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 175,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 176,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 177,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 178,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 179,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 180,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 181,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 182,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 183,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 184,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 185,status = "displayed", created_at = "2009-01-07", who = "tdreszer";
insert into project_status_logs set project_id = 100,status = "displayed", created_at = "2008-11-25", who = "tdreszer";
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x . > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x . > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x . > upload_error 2>&1 &
2009-02-24 Yale problems with multi-lined DDFs
==============================================
91,92,107,191,192,193,194,195,196,205
Edit Yale_GM12878_Input_redo.DAF/DDF for fastq only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/91 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/91 > load_error 2>&1 &
Edit Yale_GM12878_Pol2_redo.DAF/DDF for fastq only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/92 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/92 > load_error 2>&1 &
Edit YaleChipSeqRegen_redo.DDF for fastq only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > load_error 2>&1 &
Edit YaleChipSeqRegenInput_redo.DDF for fastq only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > load_error 2>&1 &
!!!!!!!! EEEEEEEEK I have been unloading all previous datasets!!! (problem is that -allowReloads unloads all previous tables generated from this dir)
Edit Yale_GM12878_Input_redo2.DAF/DDF for fastq only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/91 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/91 > load_error 2>&1 &
Edit Yale_GM12878_Pol2_redo2.DAF/DDF for fastq only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/92 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/92 > load_error 2>&1 &
Edit YaleChipSeqRegen_redo.DDF for fastq,tagAlign only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > load_error 2>&1 &
107-input must be redone without -allowReload (don't set on what has already been done) but with tables in the way (GM12878expect none to be) removed!
Also move wig/wip files out of the way
Alos move hg18.trackDb entries out of the way!
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > load_error 2>&1 &
Edit Yale_HEK293_Input_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/191 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/191 > load_error 2>&1 &
Edit Yale_HEK293_Pol2_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/192 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/192 > load_error 2>&1 &
Edit Yale_HeLa-S3_Large_Fragment_control_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/193 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/193 > load_error 2>&1 &
Edit Yale_HeLa-S3_MNase_Control_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/194 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/194 > load_error 2>&1 &
Edit Yale_HeLa-S3_MouseIgG_Control_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/195 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/195 > load_error 2>&1 &
Edit Yale_HeLa-S3_Naked_DNA_Control_redo.DAF/DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/196 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/196 > load_error 2>&1 &
Edit Yale_K562_ZNF263_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/205 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/205 > load_error 2>&1 &
!!!! Foot shooting requires redoing these
Edit YaleChipSeqRegen_redo.DDF for fastq,tagAlign only
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > load_error 2>&1 &
Edit YaleChipSeqRegenInput_redo.DDF for all
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/107 > load_error 2>&1 &
show tables like "wgEncodeYale%Peaks%";
+---------------------------------------------+
| Tables_in_hg18 (wgEncodeYale%Peaks%) |
+---------------------------------------------+
| wgEncodeYaleChIPseqPeaksGm12878Cfos |
| wgEncodeYaleChIPseqPeaksGm12878Jund |
| wgEncodeYaleChIPseqPeaksGm12878Max |
| wgEncodeYaleChIPseqPeaksGm12878Pol2 |
| wgEncodeYaleChIPseqPeaksHct116Tcf4 |
| wgEncodeYaleChIPseqPeaksHek293Pol2 |
| wgEncodeYaleChIPseqPeaksHelas3Largefragment |
| wgEncodeYaleChIPseqPeaksHelas3Mouseigg |
| wgEncodeYaleChIPseqPeaksHelas3Pol2 |
| wgEncodeYaleChIPseqPeaksHelas3ifngStat1 |
| wgEncodeYaleChIPseqPeaksK562Cfos |
| wgEncodeYaleChIPseqPeaksK562Cjun |
| wgEncodeYaleChIPseqPeaksK562Cmyc |
| wgEncodeYaleChIPseqPeaksK562Gata1 |
| wgEncodeYaleChIPseqPeaksK562Jund |
| wgEncodeYaleChIPseqPeaksK562Max |
| wgEncodeYaleChIPseqPeaksK562Nfe2 |
| wgEncodeYaleChIPseqPeaksK562Pol2 |
| wgEncodeYaleChIPseqPeaksK562Znf263 |
| wgEncodeYaleChIPseqPeaksNb4Pol2 |
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeYaleChIPseqPeaksGm12878Cfos;
| min(pValue) | max(pValue) | min(qValue) | max(qValue) |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 3.0024199485779 | 96.54231262207 |
| -1 | -1 | 0 | 90.847427368164 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 1.3117500543594 | 5.1835598945618 |
| -1 | -1 | 2.2438900470734 | 300 |
| -1 | -1 | 1.3016300201416 | 218.19619750977 |
| -1 | -1 | 1.3010300397873 | 240.68534851074 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 0 | 256.86169433594 |
| -1 | -1 | 0 | 256.23950195312 |
| -1 | -1 | 3.0335199832916 | 160.30415344238 |
| -1 | -1 | 3.0326700210571 | 168.78047180176 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 0 | 295.07369995117 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 0 | 300 |
| -1 | -1 | 0 | 300 |
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878Ctcf;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k27ac;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k27me3;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k36me3;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me2 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k9ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H4k20me1;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecCtcf ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k27ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k27me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k36me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me2 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k9ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k9me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH4k20me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecPol2b ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562Ctcf ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k27ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k27me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k36me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me2 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k9ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k9me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H4k20me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562Pol2b ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekCtcf ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k27ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k27me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k36me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me2 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me3 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k9ac ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k9me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH4k20me1 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekPol2b ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChip
| min(pValue) | max(pValue) | min(qValue) | max(qValue) |
| 6.5173001289368 | 100 | -1 | -1 |
| 4.6957998275757 | 100 | -1 | -1 |
| 0.0010000000474975 | 100 | -1 | -1 |
| 0.13099999725819 | 100 | -1 | -1 |
| 5.3927998542786 | 100 | -1 | -1 |
| 4.1328001022339 | 100 | -1 | -1 |
| 4.8709001541138 | 100 | -1 | -1 |
| 5.5492000579834 | 100 | -1 | -1 |
| 6.1911997795105 | 100 | -1 | -1 |
| 5.2214999198914 | 100 | -1 | -1 |
| 3.0020999908447 | 100 | -1 | -1 |
| 0.16380000114441 | 100 | -1 | -1 |
| 0.0026000000070781 | 100 | -1 | -1 |
| 3.0502998828888 | 100 | -1 | -1 |
| 5.4756999015808 | 100 | -1 | -1 |
| 3.1263000965118 | 100 | -1 | -1 |
| 4.057400226593 | 100 | -1 | -1 |
| 9.7910995483398 | 15.653599739075 | -1 | -1 |
| 0.10170000046492 | 100 | -1 | -1 |
| 4.1416997909546 | 100 | -1 | -1 |
| 5.2409000396729 | 100 | -1 | -1 |
| 2.2288999557495 | 100 | -1 | -1 |
| 0 | 100 | -1 | -1 |
| 0 | 15.176400184631 | -1 | -1 |
| 3.001699924469 | 100 | -1 | -1 |
| 3.0452001094818 | 100 | -1 | -1 |
| 3.1136999130249 | 100 | -1 | -1 |
| 1.9363000392914 | 100 | -1 | -1 |
| 0 | 100 | -1 | -1 |
| 0 | 100 | -1 | -1 |
| 3.1308000087738 | 100 | -1 | -1 |
| 5.5082001686096 | 100 | -1 | -1 |
| 4.5897998809814 | 100 | -1 | -1 |
| 0.7189000248909 | 15.176400184631 | -1 | -1 |
| 3.1366999149323 | 100 | -1 | -1 |
| 5.085000038147 | 100 | -1 | -1 |
| 4.6556000709534 | 100 | -1 | -1 |
| 4.564199924469 | 100 | -1 | -1 |
| 3.2702000141144 | 100 | -1 | -1 |
| 6.1206002235413 | 15.954600334167 | -1 | -1 |
| 7.5 | 100 | -1 | -1 |
| 4.246600151062 | 100 | -1 | -1 |
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksGm12878;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksK562 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksGm12878 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksK562 ;
select min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksGm12878Ctcf;
| min(pValue) | max(pValue) | min(qValue) | max(qValue) |
| 2 | 16 | -1 | -1 |
| 1.3200000524521 | 16 | -1 | -1 |
| 1.25 | 16 | -1 | -1 |
| 1.4099999666214 | 16 | -1 | -1 |
| 1.0599999427795 | 16 | -1 | -1 |
Yale new submissions 2009-02-27
===============================
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x /hive/groups/encode/dcc/pipeline/encpipeline_prod/227 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/227 > validate_error 2>&1 &
#/cluster/data/encode/pipeline/bin/encodeStatus 227 validating Not valid status!
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/227 > load_error 2>&1 &
/cluster/data/encode/pipeline/bin/encodeStatus.pl 227 loaded
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x /hive/groups/encode/dcc/pipeline/encpipeline_prod/240 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/240 > validate_error 2>&1 &
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select id,name,status,track,metadata from projects where user_id in (6,17) and status != "displayed" order by user_id,status,id;
Yale FIX PEAKS 2009-03-11
=========================
mysql> show tables like "wgEncodeYaleChIPseqPeaks%";
+---------------------------------------------+
| Tables_in_hg18 (wgEncodeYaleChIPseqPeaks%) |
+---------------------------------------------+
| wgEncodeYaleChIPseqPeaksGm12878Cfos |
| wgEncodeYaleChIPseqPeaksGm12878Jund |
| wgEncodeYaleChIPseqPeaksGm12878Max |
| wgEncodeYaleChIPseqPeaksGm12878Pol2 |
| wgEncodeYaleChIPseqPeaksHct116Tcf4 |
| wgEncodeYaleChIPseqPeaksHek293Pol2 |
| wgEncodeYaleChIPseqPeaksHelas3Largefragment |
| wgEncodeYaleChIPseqPeaksHelas3Mouseigg |
| wgEncodeYaleChIPseqPeaksHelas3Pol2 |
| wgEncodeYaleChIPseqPeaksHelas3ifngStat1 |
| wgEncodeYaleChIPseqPeaksHepg2Pol2 |
| wgEncodeYaleChIPseqPeaksHepg2Srebp1a |
| wgEncodeYaleChIPseqPeaksHepg2Srebp2 |
| wgEncodeYaleChIPseqPeaksK562Cfos |
| wgEncodeYaleChIPseqPeaksK562Cjun |
| wgEncodeYaleChIPseqPeaksK562Cmyc |
| wgEncodeYaleChIPseqPeaksK562Gata1 |
| wgEncodeYaleChIPseqPeaksK562Jund |
| wgEncodeYaleChIPseqPeaksK562Max |
| wgEncodeYaleChIPseqPeaksK562Nfe2 |
| wgEncodeYaleChIPseqPeaksK562Pol2 |
| wgEncodeYaleChIPseqPeaksK562Znf263 |
| wgEncodeYaleChIPseqPeaksNb4Pol2 |
+---------------------------------------------+
23 rows in set (0.09 sec)
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Cfos where (chromEnd - chromStart) = 0; | 280 |
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Jund where (chromEnd - chromStart) = 0; | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Max where (chromEnd - chromStart) = 0; | 405 |
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Pol2 where (chromEnd - chromStart) = 0; | 414 |
select count(*) from wgEncodeYaleChIPseqPeaksHct116Tcf4 where (chromEnd - chromStart) = 0; | 310 |
select count(*) from wgEncodeYaleChIPseqPeaksHek293Pol2 where (chromEnd - chromStart) = 0; | 361 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Largefragment where (chromEnd - chromStart) = 0;| 13 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Mouseigg where (chromEnd - chromStart) = 0; | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Pol2 where (chromEnd - chromStart) = 0; | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3ifngStat1 where (chromEnd - chromStart) = 0; | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksHepg2Pol2 where (chromEnd - chromStart) = 0; | 96 |
select count(*) from wgEncodeYaleChIPseqPeaksHepg2Srebp1a where (chromEnd - chromStart) = 0; | 57 |
select count(*) from wgEncodeYaleChIPseqPeaksHepg2Srebp2 where (chromEnd - chromStart) = 0; | 43 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Cfos where (chromEnd - chromStart) = 0; | 422 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Cjun where (chromEnd - chromStart) = 0; | 467 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Cmyc where (chromEnd - chromStart) = 0; | 270 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Gata1 where (chromEnd - chromStart) = 0; | 6 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Jund where (chromEnd - chromStart) = 0; | 2 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Max where (chromEnd - chromStart) = 0; | 349 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Nfe2 where (chromEnd - chromStart) = 0; | 172 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Pol2 where (chromEnd - chromStart) = 0; | 499 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Znf263 where (chromEnd - chromStart) = 0; | 1459 |
select count(*) from wgEncodeYaleChIPseqPeaksNb4Pol2 where (chromEnd - chromStart) = 0; | 388 |
+--------+------+----------+----------+
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Cfos; | 9094 | 0 | 174.9091 | 210.4730 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Jund; | 9053 | 25 | 442.6360 | 271.2394 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Max; | 9068 | 0 | 247.1513 | 245.1337 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Pol2; | 12229 | 0 | 363.4131 | 539.0132 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHct116Tcf4; | 8584 | 0 | 345.5130 | 364.7542 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHek293Pol2; | 12645 | 0 | 361.4106 | 525.6152 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3Largefragment;| 509 | 0 | 110.1708 | 71.2181 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3Mouseigg; | 16399 | 1 | 461.4800 | 672.5015 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3Pol2; | 74668 | 1 | 1395.050 | 2417.725 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3ifngStat1; | 86514 | 1 | 576.7702 | 742.4110 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHepg2Pol2; | 15968 | 0 | 407.6594 | 494.9533 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHepg2Srebp1a; | 1905 | 0 | 167.1914 | 161.0136 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHepg2Srebp2; | 2348 | 0 | 161.3581 | 159.9601 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Cfos; | 9052 | 0 | 214.4035 | 199.2666 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Cjun; | 8963 | 0 | 256.0553 | 239.3337 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Cmyc; | 8972 | 0 | 313.6908 | 346.7698 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Gata1; | 6932 | 0 | 336.4547 | 235.1151 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Jund; | 4893 | 0 | 379.1897 | 324.4952 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Max; | 8938 | 0 | 217.6232 | 233.3643 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Nfe2; | 10192 | 0 | 174.8999 | 214.8273 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Pol2; | 11985 | 0 | 404.6551 | 573.9241 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Znf263; | 172905 | 0 | 161.9835 | 422.8049 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksNb4Pol2; | 16249 | 0 | 434.7451 | 621.9102 |
echo "update wgEncodeYaleChIPseqPeaksGm12878Cfos set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksGm12878Jund set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksGm12878Max set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksGm12878Pol2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHct116Tcf4 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHek293Pol2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHelas3Largefragment set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHelas3Mouseigg set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHelas3Pol2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHelas3ifngStat1 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHepg2Pol2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHepg2Srebp1a set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksHepg2Srebp2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Cfos set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Cjun set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Cmyc set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Gata1 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Jund set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Max set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Nfe2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Pol2 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksK562Znf263 set chromStart = chromStart - 1" | hgsql hg18
echo "update wgEncodeYaleChIPseqPeaksNb4Pol2 set chromStart = chromStart - 1" | hgsql hg18
+----------+----------+
| Before=0 | After=1 |
+----------+----------+
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Cfos where (chromEnd - chromStart) = 1; | 280 | 280 |
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Jund where (chromEnd - chromStart) = 1; | 0 | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Max where (chromEnd - chromStart) = 1; | 405 | 405 |
select count(*) from wgEncodeYaleChIPseqPeaksGm12878Pol2 where (chromEnd - chromStart) = 1; | 414 | 414 |
select count(*) from wgEncodeYaleChIPseqPeaksHct116Tcf4 where (chromEnd - chromStart) = 1; | 310 | 310 |
select count(*) from wgEncodeYaleChIPseqPeaksHek293Pol2 where (chromEnd - chromStart) = 1; | 361 | 361 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Largefragment where (chromEnd - chromStart) = 1;| 13 | 13 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Mouseigg where (chromEnd - chromStart) = 1; | 0 | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Pol2 where (chromEnd - chromStart) = 1; | 0 | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksHelas3ifngStat1 where (chromEnd - chromStart) = 1; | 0 | 0 |
select count(*) from wgEncodeYaleChIPseqPeaksHepg2Pol2 where (chromEnd - chromStart) = 1; | 96 | 96 |
select count(*) from wgEncodeYaleChIPseqPeaksHepg2Srebp1a where (chromEnd - chromStart) = 1; | 57 | 57 |
select count(*) from wgEncodeYaleChIPseqPeaksHepg2Srebp2 where (chromEnd - chromStart) = 1; | 43 | 43 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Cfos where (chromEnd - chromStart) = 1; | 422 | 422 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Cjun where (chromEnd - chromStart) = 1; | 467 | 467 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Cmyc where (chromEnd - chromStart) = 1; | 270 | 270 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Gata1 where (chromEnd - chromStart) = 1; | 6 | 6 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Jund where (chromEnd - chromStart) = 1; | 2 | 2 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Max where (chromEnd - chromStart) = 1; | 349 | 349 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Nfe2 where (chromEnd - chromStart) = 1; | 172 | 172 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Pol2 where (chromEnd - chromStart) = 1; | 499 | 499 |
select count(*) from wgEncodeYaleChIPseqPeaksK562Znf263 where (chromEnd - chromStart) = 1; | 1459 | 1459 | +--------+------+----------+----------++--------+------+----------+----------+
select count(*) from wgEncodeYaleChIPseqPeaksNb4Pol2 where (chromEnd - chromStart) = 1; | 388 | 388 | + Before ++ After +
+----------+----------+ | max | min | avg | sd || max | min | avg | sd |
+--------+------+----------+----------++--------+------+----------+----------+
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Cfos; | 9094 | 0 | 174.9091 | 210.4730 || 9095 | 1 | 175.9091 | 210.4730 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Jund; | 9053 | 25 | 442.6360 | 271.2394 || 9054 | 26 | 443.6360 | 271.2394 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Max; | 9068 | 0 | 247.1513 | 245.1337 || 9069 | 1 | 248.1513 | 245.1337 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksGm12878Pol2; | 12229 | 0 | 363.4131 | 539.0132 || 12230 | 1 | 364.4131 | 539.0132 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHct116Tcf4; | 8584 | 0 | 345.5130 | 364.7542 || 8585 | 1 | 346.5130 | 364.7542 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHek293Pol2; | 12645 | 0 | 361.4106 | 525.6152 || 12646 | 1 | 362.4106 | 525.6152 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3Largefragment;| 509 | 0 | 110.1708 | 71.2181 || 510 | 1 | 111.1708 | 71.2181 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3Mouseigg; | 16399 | 1 | 461.4800 | 672.5015 || 16400 | 2 | 462.4800 | 672.5015 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3Pol2; | 74668 | 1 | 1395.050 | 2417.725 || 74669 | 2 | 1396.050 | 2417.725 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHelas3ifngStat1; | 86514 | 1 | 576.7702 | 742.4110 || 86515 | 2 | 577.7702 | 742.4110 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHepg2Pol2; | 15968 | 0 | 407.6594 | 494.9533 || 15969 | 1 | 408.6594 | 494.9533 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHepg2Srebp1a; | 1905 | 0 | 167.1914 | 161.0136 || 1906 | 1 | 168.1914 | 161.0136 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksHepg2Srebp2; | 2348 | 0 | 161.3581 | 159.9601 || 2349 | 1 | 162.3581 | 159.9601 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Cfos; | 9052 | 0 | 214.4035 | 199.2666 || 9053 | 1 | 215.4035 | 199.2666 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Cjun; | 8963 | 0 | 256.0553 | 239.3337 || 8964 | 1 | 257.0553 | 239.3337 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Cmyc; | 8972 | 0 | 313.6908 | 346.7698 || 8973 | 1 | 314.6908 | 346.7698 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Gata1; | 6932 | 0 | 336.4547 | 235.1151 || 6933 | 1 | 337.4547 | 235.1151 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Jund; | 4893 | 0 | 379.1897 | 324.4952 || 4894 | 1 | 380.1897 | 324.4952 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Max; | 8938 | 0 | 217.6232 | 233.3643 || 8939 | 1 | 218.6232 | 233.3643 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Nfe2; | 10192 | 0 | 174.8999 | 214.8273 || 10193 | 1 | 175.8999 | 214.8273 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Pol2; | 11985 | 0 | 404.6551 | 573.9241 || 11986 | 1 | 405.6551 | 573.9241 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksK562Znf263; | 172905 | 0 | 161.9835 | 422.8049 || 172906 | 1 | 162.9835 | 422.8049 |
select max(chromEnd - chromStart) max, min(chromEnd - chromStart) min, avg(chromEnd - chromStart) avg, stddev(chromEnd - chromStart) sd from wgEncodeYaleChIPseqPeaksNb4Pol2; | 16249 | 0 | 434.7451 | 621.9102 || 16250 | 1 | 435.7451 | 621.9102 |
+--------+------+----------+----------++--------+------+----------+----------+
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/276 > load_error 2>&1 &
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 loaded
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 displayed
Yale Reload Signals Input 2009-03-21 Hive Broken
====================================
show tables like "wgEncodeYaleNew%";
| wgEncodeYaleNewChIPseqSignalGm12878Input |
| wgEncodeYaleNewChIPseqSignalHct116Input |
| wgEncodeYaleNewChIPseqSignalHek293Input |
| wgEncodeYaleNewChIPseqSignalHelas3Input |
| wgEncodeYaleNewChIPseqSignalHelas3ifngInput |
| wgEncodeYaleNewChIPseqSignalHepg2Input |
| wgEncodeYaleNewChIPseqSignalK562Input |
| wgEncodeYaleNewChIPseqSignalNb4Input |
rename table wgEncodeYaleChIPseqSignalGm12878Input to wgEncodeOldYaleChIPseqSignalGm12878Input ;
rename table wgEncodeYaleChIPseqSignalHct116Input to wgEncodeOldYaleChIPseqSignalHct116Input ;
rename table wgEncodeYaleChIPseqSignalHek293Input to wgEncodeOldYaleChIPseqSignalHek293Input ;
rename table wgEncodeYaleChIPseqSignalHelas3Input to wgEncodeOldYaleChIPseqSignalHelas3Input ;
rename table wgEncodeYaleChIPseqSignalHelas3ifngInput to wgEncodeOldYaleChIPseqSignalHelas3ifngInput;
rename table wgEncodeYaleChIPseqSignalHepg2Input to wgEncodeOldYaleChIPseqSignalHepg2Input ;
rename table wgEncodeYaleChIPseqSignalK562Input to wgEncodeOldYaleChIPseqSignalK562Input ;
rename table wgEncodeYaleChIPseqSignalNb4Input to wgEncodeOldYaleChIPseqSignalNb4Input ;
rename table wgEncodeYaleNewChIPseqSignalGm12878Input to wgEncodeYaleChIPseqSignalGm12878Input ;
rename table wgEncodeYaleNewChIPseqSignalHct116Input to wgEncodeYaleChIPseqSignalHct116Input ;
rename table wgEncodeYaleNewChIPseqSignalHek293Input to wgEncodeYaleChIPseqSignalHek293Input ;
rename table wgEncodeYaleNewChIPseqSignalHelas3Input to wgEncodeYaleChIPseqSignalHelas3Input ;
rename table wgEncodeYaleNewChIPseqSignalHelas3ifngInput to wgEncodeYaleChIPseqSignalHelas3ifngInput;
rename table wgEncodeYaleNewChIPseqSignalHepg2Input to wgEncodeYaleChIPseqSignalHepg2Input ;
rename table wgEncodeYaleNewChIPseqSignalK562Input to wgEncodeYaleChIPseqSignalK562Input ;
rename table wgEncodeYaleNewChIPseqSignalNb4Input to wgEncodeYaleChIPseqSignalNb4Input ;
ls wgEncodeYaleChIPseqSignalGm12878Input.wig.gz
ls wgEncodeYaleChIPseqSignalHelas3ifngInput.wig.gz
ls wgEncodeYaleChIPseqSignalHct116Input.wig.gz
ls wgEncodeYaleChIPseqSignalHepg2Input.wig.gz
ls wgEncodeYaleChIPseqSignalHek293Input.wig.gz
ls wgEncodeYaleChIPseqSignalK562Input.wig.gz
ls wgEncodeYaleChIPseqSignalHelas3Input.wig.gz
ls wgEncodeYaleChIPseqSignalNb4Input.wig.gz
mv wgEncodeYaleChIPseqSignalGm12878Input.wig.gz wgEncodeYaleChIPseqSignalGm12878Input.wig.gz.old
mv wgEncodeYaleChIPseqSignalHelas3ifngInput.wig.gz wgEncodeYaleChIPseqSignalHelas3ifngInput.wig.gz.old
mv wgEncodeYaleChIPseqSignalHct116Input.wig.gz wgEncodeYaleChIPseqSignalHct116Input.wig.gz.old
mv wgEncodeYaleChIPseqSignalHepg2Input.wig.gz wgEncodeYaleChIPseqSignalHepg2Input.wig.gz.old
mv wgEncodeYaleChIPseqSignalHek293Input.wig.gz wgEncodeYaleChIPseqSignalHek293Input.wig.gz.old
mv wgEncodeYaleChIPseqSignalK562Input.wig.gz wgEncodeYaleChIPseqSignalK562Input.wig.gz.old
mv wgEncodeYaleChIPseqSignalHelas3Input.wig.gz wgEncodeYaleChIPseqSignalHelas3Input.wig.gz.old
mv wgEncodeYaleChIPseqSignalNb4Input.wig.gz wgEncodeYaleChIPseqSignalNb4Input.wig.gz.old
mv wgEncodeYaleNewChIPseqSignalGm12878Input.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878Input.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalHelas3ifngInput.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3ifngInput.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalHct116Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHct116Input.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalHepg2Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHepg2Input.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalHek293Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHek293Input.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalK562Input.bedGraph4.gz wgEncodeYaleChIPseqSignalK562Input.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalHelas3Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3Input.bedGraph4.gz
mv wgEncodeYaleNewChIPseqSignalNb4Input.bedGraph4.gz wgEncodeYaleChIPseqSignalNb4Input.bedGraph4.gz
### Because tables are already on RR, the safest way of doing this so that new settings don't overwrite old is to use new table names!
rename table wgEncodeYaleChIPseqSignalGm12878Input to wgEncodeYaleChIPseqSignalGm12878InputBg ;
rename table wgEncodeYaleChIPseqSignalHct116Input to wgEncodeYaleChIPseqSignalHct116InputBg ;
rename table wgEncodeYaleChIPseqSignalHek293Input to wgEncodeYaleChIPseqSignalHek293InputBg ;
rename table wgEncodeYaleChIPseqSignalHelas3Input to wgEncodeYaleChIPseqSignalHelas3InputBg ;
rename table wgEncodeYaleChIPseqSignalHelas3ifngInput to wgEncodeYaleChIPseqSignalHelas3ifngInputBg;
rename table wgEncodeYaleChIPseqSignalHepg2Input to wgEncodeYaleChIPseqSignalHepg2InputBg ;
rename table wgEncodeYaleChIPseqSignalK562Input to wgEncodeYaleChIPseqSignalK562InputBg ;
rename table wgEncodeYaleChIPseqSignalNb4Input to wgEncodeYaleChIPseqSignalNb4InputBg ;
rename table wgEncodeOldYaleChIPseqSignalGm12878Input to wgEncodeYaleChIPseqSignalGm12878Input ;
rename table wgEncodeOldYaleChIPseqSignalHct116Input to wgEncodeYaleChIPseqSignalHct116Input ;
rename table wgEncodeOldYaleChIPseqSignalHek293Input to wgEncodeYaleChIPseqSignalHek293Input ;
rename table wgEncodeOldYaleChIPseqSignalHelas3Input to wgEncodeYaleChIPseqSignalHelas3Input ;
rename table wgEncodeOldYaleChIPseqSignalHelas3ifngInput to wgEncodeYaleChIPseqSignalHelas3ifngInput;
rename table wgEncodeOldYaleChIPseqSignalHepg2Input to wgEncodeYaleChIPseqSignalHepg2Input ;
rename table wgEncodeOldYaleChIPseqSignalK562Input to wgEncodeYaleChIPseqSignalK562Input ;
rename table wgEncodeOldYaleChIPseqSignalNb4Input to wgEncodeYaleChIPseqSignalNb4Input ;
mv wgEncodeYaleChIPseqSignalGm12878Input.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878InputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHelas3ifngInput.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3ifngInputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHct116Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHct116InputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHepg2Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHepg2InputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHek293Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHek293InputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalK562Input.bedGraph4.gz wgEncodeYaleChIPseqSignalK562InputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHelas3Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3InputBg.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalNb4Input.bedGraph4.gz wgEncodeYaleChIPseqSignalNb4InputBg.bedGraph4.gz
# Not going to move these back. Old foles should not be on the downloads page.
#mv wgEncodeYaleChIPseqSignalGm12878Input.wig.gz.old wgEncodeYaleChIPseqSignalGm12878Input.wig.gz
#mv wgEncodeYaleChIPseqSignalHelas3ifngInput.wig.gz.old wgEncodeYaleChIPseqSignalHelas3ifngInput.wig.gz
#mv wgEncodeYaleChIPseqSignalHct116Input.wig.gz.old wgEncodeYaleChIPseqSignalHct116Input.wig.gz
#mv wgEncodeYaleChIPseqSignalHepg2Input.wig.gz.old wgEncodeYaleChIPseqSignalHepg2Input.wig.gz
#mv wgEncodeYaleChIPseqSignalHek293Input.wig.gz.old wgEncodeYaleChIPseqSignalHek293Input.wig.gz
#mv wgEncodeYaleChIPseqSignalK562Input.wig.gz.old wgEncodeYaleChIPseqSignalK562Input.wig.gz
#mv wgEncodeYaleChIPseqSignalHelas3Input.wig.gz.old wgEncodeYaleChIPseqSignalHelas3Input.wig.gz
#mv wgEncodeYaleChIPseqSignalNb4Input.wig.gz.old wgEncodeYaleChIPseqSignalNb4Input.wig.gz
/cluster/data/encode/pipeline/bin/encodeStatus.pl 279 displayed
Fix Yale fastq's
================
| 12 | YHD_HeLa-S3_Pol2 | released |
| 13 | YHD_HeLa-S3_IFNg_STAT1 | released |
| 14 | YHD_HeLa-S3_Input | released |
| 15 | YHD_HeLa-S3_IFNg_Input | released |
| 16 | YHD_K562_Pol2 | released |
| 17 | YHD_K562_Input | released |
| 18 | YHD_NB4_Pol2 | released |
| 19 | YHD_NB4_Input | released |
| 68 | YHD_K562_Fos | released |
| 69 | YHD_K562_Myc | released |
| 72 | YHD_K562_Jun | released |
| 91 | YHD_GM12878_Input | released |
| 92 | YHD_GM12878_Pol2 | released |
| 94 | YHD_GM12878_c-Fos | released |
| 189 | YHD_K562_NF-E2 | released |
| 190 | YHD_GM12878_Max | released |
| 191 | YHD_HEK293_Input | released |
| 192 | YHD_HEK293_Pol2 | released |
| 193 | YHD_HeLa-S3_Large_Fragment_Control | released |
| 194 | YHD_HeLa-S3_MNase_Control | released |
| 195 | YHD_HeLa-S3_MouseIgG_Control | released |
| 196 | YHD_HeLa-S3_Naked_DNA_Control | released |
| 205 | YHD_K562_ZNF263 | released |
| 224 | YHD_HCT-116_Input | released |
| 225 | YHD_HCT-116_TCF4 | released |
| 226 | YHD_K562_Max | released |
| 227 | YHD_K562_GATA-1 | released |
| 238 | YHD_K562_JunD | released |
| 239 | YHD_GM12878_JunD | released |
| 240 | YHD_HepG2_Input | released |
| 241 | YHD_HepG2_Pol2 | released |
| 242 | YHD_HepG2_SREBP1A | released |
| 243 | YHD_HepG2_SREBP2 | released |
| 276 | YHD_K562_PolyA_RNA | displayed |
14/HeLa-S3_Input_DNA_sequence_rep1_lane*.fastq RawData HeLa-S3 Input 1 GSE12781
12/HeLa-S3_Pol2_sequence_rep1_lane*.fastq RawData HeLa-S3 Pol2 1 GSE12781
12/HeLa-S3_Pol2_sequence_rep2_lane*.fastq RawData HeLa-S3 Pol2 2 GSE12781
12/HeLa-S3_Pol2_sequence_rep3_lane*.fastq RawData HeLa-S3 Pol2 3 GSE12781
193/Data/Yale_HeLa-S3_Large_Fragment_sequence_rep1_*.fastq RawData HeLa-S3 Large_Fragment 1
193/Data/Yale_HeLa-S3_Large_Fragment_sequence_rep2_*.fastq RawData HeLa-S3 Large_Fragment 2
194/Data/Yale_HeLa-S3_MNase_sequence_rep1_*.fastq RawData HeLa-S3 MNase 1
194/Data/Yale_HeLa-S3_MNase_sequence_rep2_*.fastq RawData HeLa-S3 MNase 2
195/Data/Yale_HeLa-S3_MouseIgG_sequence_rep1_*.fastq RawData HeLa-S3 Mouse_IgG 1
195/Data/Yale_HeLa-S3_MouseIgG_sequence_rep2_*.fastq RawData HeLa-S3 Mouse_IgG 2
196/Data/Yale_HeLa-S3_Naked_DNA_sequence_rep1_*.fastq RawData HeLa-S3 Naked_DNA 1
196/Data/Yale_HeLa-S3_Naked_DNA_sequence_rep2_*.fastq RawData HeLa-S3 Naked_DNA 2
196/Data/Yale_HeLa-S3_Naked_DNA_sequence_rep3_*.fastq RawData HeLa-S3 Naked_DNA 3
15/HeLa-S3_IFNg_Input_sequence_rep1_lane*.fastq RawData HeLa-S3 Input 1 GSE12782
13/IFNg_HeLa-S3_STAT1_sequence_rep1_lane*.fastq RawData HeLa-S3_IFNg STAT1 1 GSE12782
13/IFNg_HeLa-S3_STAT1_sequence_rep2_lane*.fastq RawData HeLa-S3_IFNg STAT1 2 GSE12782
17/Data/Yale_K562_Input_sequence_rep1*.fastq RawData K562 Input 1
16/Data/Yale_K562_Pol2_sequence_rep1*.fastq RawData K562 Pol2 1
16/Data/Yale_K562_Pol2_sequence_rep2*.fastq RawData K562 Pol2 2
68/Data/Yale_K562_Fos_sequence_rep1_FC20GEE_062208_s_4.fastq RawData K562 c-Fos 1
68/Data/Yale_K562_Fos_sequence_rep2_FC20GEE_062208_s_5.fastq RawData K562 c-Fos 2
68/Data/Yale_K562_Fos_sequence_rep3_FC20GEE_062208_s_6.fastq RawData K562 c-Fos 3
69/Data/Yale_K562_Myc_sequence_rep1_FC20GEE_062208_s_7.fastq RawData K562 c-Myc 1
69/Data/Yale_K562_Myc_sequence_rep2_FC20GEE_062208_s_8.fastq RawData K562 c-Myc 2
72/Data/Yale_K562_Jun_sequence_rep1*.fastq RawData K562 c-Jun 1
72/Data/Yale_K562_Jun_sequence_rep2*.fastq RawData K562 c-Jun 2
189/Data/Yale_K562_NF-E2_sequence_rep1_FC30B51AA_082608_s_3.fastq RawData K562 NF-E2 1
189/Data/Yale_K562_NF-E2_sequence_rep2_FC30B51AA_082608_s_5.fastq RawData K562 NF-E2 2
205/Data/Yale_K562_ZNF263_sequence_rep1_*.fastq RawData K562 ZNF263 1
205/Data/Yale_K562_ZNF263_sequence_rep2_*.fastq RawData K562 ZNF263 2
226/Data/Yale_K562_Max_sequence_rep1_*.fastq RawData K562 Max 1
226/Data/Yale_K562_Max_sequence_rep2_*.fastq RawData K562 Max 2
227/Data/Yale_K562_GATA-1_sequence_rep1_*.fastq RawData K562 GATA-1 1
227/Data/Yale_K562_GATA-1_sequence_rep2_*.fastq RawData K562 GATA-1 2
238/Data/Yale_K562_JunD_sequence_rep1_*.fastq RawData K562 JunD 1
238/Data/Yale_K562_JunD_sequence_rep2_*.fastq RawData K562 JunD 2
91/Data/Yale_GM12878_Input_*.fastq RawData GM12878 Input 1
92/Data/Yale_GM12878_Pol2_sequence_rep1_*.fastq RawData GM12878 Pol2 1
92/Data/Yale_GM12878_Pol2_sequence_rep2_*.fastq RawData GM12878 Pol2 2
94/Data/Yale_GM12878_c-Fos_sequence_rep1_FC20GEE_062208_s_1.fastq RawData GM12878 c-Fos 1
94/Data/Yale_GM12878_c-Fos_sequence_rep2_FC20GEE_062208_s_2.fastq RawData GM12878 c-Fos 2
94/Data/Yale_GM12878_c-Fos_sequence_rep3_FC20GEE_062208_s_3.fastq RawData GM12878 c-Fos 3
190/Data/Yale_GM12878_Max_sequence_rep1_FC30H99AA_102408_s_1.fastq RawData GM12878 Max 1
190/Data/Yale_GM12878_Max_sequence_rep2_FC30H99AA_102408_s_2.fastq RawData GM12878 Max 2
239/Data/Yale_GM12878_JunD_sequence_rep1_*.fastq RawData GM12878 JunD 1
239/Data/Yale_GM12878_JunD_sequence_rep2_*.fastq RawData GM12878 JunD 2
19/Data/Yale_NB4_Input_sequence_rep1*.fastq RawData NB4 Input 1
18/Data/Yale_NB4_Pol2_sequence_rep1*.fastq RawData NB4 Pol2 1
18/Data/Yale_NB4_Pol2_sequence_rep2*.fastq RawData NB4 Pol2 2
18/Data/Yale_NB4_Pol2_sequence_rep3*.fastq RawData NB4 Pol2 3
191/Data/Yale_HEK293_Input_sequence_*.fastq RawData HEK293 Input 1
192/Data/Yale_HEK293_Pol2_sequence_rep1_*.fastq RawData HEK293 Pol2 1
192/Data/Yale_HEK293_Pol2_sequence_rep2_*.fastq RawData HEK293 Pol2 2
192/Data/Yale_HEK293_Pol2_sequence_rep3_*.fastq RawData HEK293 Pol2 3
224/Data/Yale_HCT-116_Input_sequence_*.fastq RawData HCT-116 Input 1
225/Data/Yale_HCT-116_TCF4_sequence_rep1_*.fastq RawData HCT-116 TCF4 1
225/Data/Yale_HCT-116_TCF4_sequence_rep2_*.fastq RawData HCT-116 TCF4 2
240/Data/Yale_HepG2_Input_sequence_rep1_*.fastq RawData HepG2 Input 1
240/Data/Yale_HepG2_Input_sequence_rep2_*.fastq RawData HepG2 Input 2
240/Data/Yale_HepG2_Input_sequence_rep3_*.fastq RawData HepG2 Input 3
241/Data/Yale_HepG2_Pol2_sequence_rep1_*.fastq RawData HepG2 Pol2 1
241/Data/Yale_HepG2_Pol2_sequence_rep2_*.fastq RawData HepG2 Pol2 2
241/Data/Yale_HepG2_Pol2_sequence_rep3_*.fastq RawData HepG2 Pol2 3
242/Data/Yale_HepG2_SREBP1A_sequence_rep1_*.fastq RawData HepG2 SREBP1A 1
242/Data/Yale_HepG2_SREBP1A_sequence_rep2_*.fastq RawData HepG2 SREBP1A 2
242/Data/Yale_HepG2_SREBP1A_sequence_rep3_*.fastq RawData HepG2 SREBP1A 3
243/Data/Yale_HepG2_SREBP2_sequence_rep1_*.fastq RawData HepG2 SREBP2 1
243/Data/Yale_HepG2_SREBP2_sequence_rep2_*.fastq RawData HepG2 SREBP2 2
243/Data/Yale_HepG2_SREBP2_sequence_rep3_*.fastq RawData HepG2 SREBP2 3
276/Data/YHD_K562_PolyA_RNA_sequence*.fastq RawData K562 1
# Determine filter limits for peaks:
| wgEncodeYaleChIPseqPeaksGm12878Cfos |
| wgEncodeYaleChIPseqPeaksGm12878Jund |
| wgEncodeYaleChIPseqPeaksGm12878Max |
| wgEncodeYaleChIPseqPeaksGm12878Pol2 |
| wgEncodeYaleChIPseqPeaksGm12878Pol3 |
| wgEncodeYaleChIPseqPeaksHct116Tcf4 |
| wgEncodeYaleChIPseqPeaksHek293Pol2 |
| wgEncodeYaleChIPseqPeaksHelas3Cfos |
| wgEncodeYaleChIPseqPeaksHelas3Cmyc |
| wgEncodeYaleChIPseqPeaksHelas3Largefragment |
| wgEncodeYaleChIPseqPeaksHelas3Max |
| wgEncodeYaleChIPseqPeaksHelas3Mouseigg |
| wgEncodeYaleChIPseqPeaksHelas3Pol2 |
| wgEncodeYaleChIPseqPeaksHelas3ifngStat1 |
| wgEncodeYaleChIPseqPeaksHepg2Pol2 |
| wgEncodeYaleChIPseqPeaksHepg2Srebp1a |
| wgEncodeYaleChIPseqPeaksHepg2Srebp2 |
| wgEncodeYaleChIPseqPeaksK562Cfos |
| wgEncodeYaleChIPseqPeaksK562Cjun |
| wgEncodeYaleChIPseqPeaksK562Cmyc |
| wgEncodeYaleChIPseqPeaksK562Gata1 |
| wgEncodeYaleChIPseqPeaksK562Jund |
| wgEncodeYaleChIPseqPeaksK562Max |
| wgEncodeYaleChIPseqPeaksK562Nfe2 |
| wgEncodeYaleChIPseqPeaksK562Pol2 |
| wgEncodeYaleChIPseqPeaksK562Rad21 |
| wgEncodeYaleChIPseqPeaksK562Xrcc4 |
| wgEncodeYaleChIPseqPeaksK562Znf263 |
| wgEncodeYaleChIPseqPeaksNb4Pol2 |
| wgEncodeYaleChIPseqRel2PeaksGm12878Cfos |
| wgEncodeYaleChIPseqRel2PeaksGm12878Jund |
| wgEncodeYaleChIPseqRel2PeaksGm12878Max |
| wgEncodeYaleChIPseqRel2PeaksGm12878Pol2 |
| wgEncodeYaleChIPseqRel2PeaksHct116Tcf4 |
| wgEncodeYaleChIPseqRel2PeaksHek293Pol2 |
| wgEncodeYaleChIPseqRel2PeaksHelas3Pol2 |
| wgEncodeYaleChIPseqRel2PeaksK562Cfos |
| wgEncodeYaleChIPseqRel2PeaksK562Cjun |
| wgEncodeYaleChIPseqRel2PeaksK562Cmyc |
| wgEncodeYaleChIPseqRel2PeaksK562Gata1 |
| wgEncodeYaleChIPseqRel2PeaksK562Jund |
| wgEncodeYaleChIPseqRel2PeaksK562Max |
| wgEncodeYaleChIPseqRel2PeaksK562Nfe2 |
| wgEncodeYaleChIPseqRel2PeaksK562Pol2 |
| wgEncodeYaleChIPseqRel2PeaksK562Znf263 |
| wgEncodeYaleChIPseqRel2PeaksNb4Pol2 |
select min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeYaleChIPseqPeaksK562Xrcc4;
+------------------+------------------+-----------------+-----------------+-----------------+-----------------+
| min(signalValue) | max(signalValue) | min(pValue) | max(pValue) | min(qValue) | max(qValue) |
+------------------+------------------+-----------------+-----------------+-----------------+-----------------+
| 1.3901400566101 | 611.30426025391 | 1.3034399747849 | 124.44661712646 | 3.311320066452 | 129.08288574219 | wgEncodeYaleChIPseqPeaksGm12878Pol3;
| 1.2307300567627 | 1777.0512695312 | 1.3011900186539 | 172.99728393555 | 1.7770600318909 | 177.92849731445 | wgEncodeYaleChIPseqPeaksHelas3Cfos;
| 1.2226899862289 | 1352.9223632812 | 1.3019100427628 | 260.36569213867 | 1.8232300281525 | 265.30029296875 | wgEncodeYaleChIPseqPeaksHelas3Cmyc;
| 1.1304099559784 | 733.25946044922 | 1.3024799823761 | 283.87057495117 | 1.8091399669647 | 288.8776550293 | wgEncodeYaleChIPseqPeaksHelas3Max;
| 1.1479400396347 | 1420.5920410156 | 1.303789973259 | 222.53610229492 | 1.4720799922943 | 226.95211791992 | wgEncodeYaleChIPseqPeaksK562Rad21;
| 1.2304999828339 | 446.61828613281 | 1.3087400197983 | 207.92915344238 | 2.5831201076508 | 211.45474243164 | wgEncodeYaleChIPseqPeaksK562Xrcc4;
| 3.0079400539398 | 280.51501464844 | -1 | -1 | 1.3117500543594 | 5.1835598945618 | wgEncodeYaleChIPseqPeaksHelas3Largefragment; old peaks
| 5.001570224762 | 1456.5600585938 | -1 | -1 | 2.2438900470734 | 300 | wgEncodeYaleChIPseqPeaksHelas3Mouseigg; old peaks
| 1.0036300420761 | 1899.4759521484 | -1 | -1 | 1.3010300397873 | 240.68534851074 | wgEncodeYaleChIPseqPeaksHelas3ifngStat1; old peaks
| 1.5272200107574 | 10593.700195312 | -1 | -1 | 1.3073300123215 | 300 | wgEncodeYaleChIPseqPeaksHepg2Pol2; old peaks
| 1.4039800167084 | 9397.6904296875 | -1 | -1 | 1.301059961319 | 148.73680114746 | wgEncodeYaleChIPseqPeaksHepg2Srebp1a; old peaks
| 1.3785300254822 | 4717.8598632812 | -1 | -1 | 1.3010499477386 | 201.95668029785 | wgEncodeYaleChIPseqPeaksHepg2Srebp2; old peaks
| 0.26910999417305 | 9750.6943359375 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksGm12878Cfos; old peaks
| 1.331200003624 | 2248.4096679688 | 1.301059961319 | 300 | 1.9688999652863 | 300 | wgEncodeYaleChIPseqRel2PeaksGm12878Cfos;
| 1.5449999570847 | 206.34483337402 | -1 | -1 | 3.0024199485779 | 96.54231262207 | wgEncodeYaleChIPseq PeaksGm12878Jund; old peaks
| 1.2527199983597 | 7042.3569335938 | 1.3050899505615 | 96.54231262207 | 1.5731699466705 | 300 | wgEncodeYaleChIPseqRel2PeaksGm12878Jund;
| 0.23410999774933 | 4674.267578125 | -1 | -1 | 0 | 90.847427368164 | wgEncodeYaleChIPseq PeaksGm12878Max; old peaks
| 1.1049200296402 | 2727.3859863281 | 1.3020499944687 | 85.993377685547 | 2.049770116806 | 90.847427368164 | wgEncodeYaleChIPseqRel2PeaksGm12878Max;
| 0.08718000352383 | 2348.5390625 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksGm12878Pol2; old peaks
| 1.2164100408554 | 1979.5601806641 | 1.3021899461746 | 300 | 1.8839600086212 | 300 | wgEncodeYaleChIPseqRel2PeaksGm12878Pol2;
| 0.24221999943256 | 6968.115234375 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksHct116Tcf4; old peaks
| 1.1837500333786 | 2858.4267578125 | 1.302060008049 | 300 | 1.4207600355148 | 300 | wgEncodeYaleChIPseqRel2PeaksHct116Tcf4;
| 0.07487999647856 | 4214.2016601562 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksHek293Pol2; old peaks
| 1.3379199504852 | 1814.4339599609 | 1.3035399913788 | 300 | 1.6756000518799 | 300 | wgEncodeYaleChIPseqRel2PeaksHek293Pol2;
| 1.0000100135803 | 1807.1166992188 | -1 | -1 | 1.3016300201416 | 218.19619750977 | wgEncodeYaleChIPseq PeaksHelas3Pol2; old peaks
| -0.3072899878025 | 1137.6721191406 | 1.301059961319 | 231.30393981934 | 1.7342599630356 | 233.51809692383 | wgEncodeYaleChIPseqRel2PeaksHelas3Pol2;
| 0.18659999966621 | 11096.375976562 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksK562Cfos; old peaks
| 1.1689599752426 | 872.79962158203 | 1.3033900260925 | 300 | 1.7389299869537 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Cfos;
| 0.11000999808311 | 13153.647460938 | -1 | -1 | 0 | 256.86169433594 | wgEncodeYaleChIPseq PeaksK562Cjun; old peaks
| 1.1969499588013 | 327.81936645508 | 1.3026900291443 | 229.9097442627 | 1.7244700193405 | 234.90943908691 | wgEncodeYaleChIPseqRel2PeaksK562Cjun;
| 0.05459000170231 | 5889.5512695312 | -1 | -1 | 0 | 256.23950195312 | wgEncodeYaleChIPseq PeaksK562Cmyc; old peaks
| 1.2487000226974 | 203.55351257324 | 1.3012200593948 | 257.67834472656 | 1.8194299936295 | 262.02362060547 | wgEncodeYaleChIPseqRel2PeaksK562Cmyc;
| 1.2489099502563 | 6080.392578125 | -1 | -1 | 3.0335199832916 | 160.30415344238 | wgEncodeYaleChIPseq PeaksK562Gata1; old peaks
| 1.0990400314331 | 18241.177734375 | 1.3014600276947 | 160.30415344238 | 1.4422600269318 | 164.9938659668 | wgEncodeYaleChIPseqRel2PeaksK562Gata1;
| 1.1775399446487 | 2517.7607421875 | -1 | -1 | 3.0326700210571 | 168.78047180176 | wgEncodeYaleChIPseq PeaksK562Jund; old peaks
| 1.181480050087 | 47.822288513184 | 1.3025200366974 | 240.95959472656 | 2.1446800231934 | 245.24108886719 | wgEncodeYaleChIPseqRel2PeaksK562Jund;
| 0.06341999769211 | 8959.7763671875 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksK562Max; old peaks
| 1.2188500165939 | 133.69340515137 | 1.3030099868774 | 213.0196685791 | 1.827919960022 | 217.79626464844 | wgEncodeYaleChIPseqRel2PeaksK562Max;
| 0.129109993577 | 9554.4775390625 | -1 | -1 | 0 | 295.07369995117 | wgEncodeYaleChIPseq PeaksK562Nfe2; old peaks
| 1.2230999469757 | 77.342399597168 | 1.3015500307083 | 297.89761352539 | 1.8038400411606 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Nfe2;
| 0.05313000082970 | 5486.4291992188 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksK562Pol2; old peaks
| 1.1640499830246 | 2476.1047363281 | 1.303200006485 | 300 | 1.7722599506378 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Pol2;
| 0.09604000300169 | 14944.065429688 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksK562Znf263; old peaks
| 1.170009970665 | 10674.33203125 | 1.3010300397873 | 300 | 1.6494699716568 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Znf263;
| 0.08269000053406 | 3450.4016113281 | -1 | -1 | 0 | 300 | wgEncodeYaleChIPseq PeaksNb4Pol2; old peaks
| 1.2452100515366 | 3450.4016113281 | 1.3032200336456 | 300 | 1.5723099708557 | 300 | wgEncodeYaleChIPseqRel2PeaksNb4Pol2;
+------------------+------------------+-----------------+-----------------+-----------------+-----------------+
Just new peaks:
| 1.3901400566101 | 611.30426025391 | 1.3034399747849 | 124.44661712646 | 3.311320066452 | 129.08288574219 | wgEncodeYaleChIPseqPeaksGm12878Pol3;
| 1.2307300567627 | 1777.0512695312 | 1.3011900186539 | 172.99728393555 | 1.7770600318909 | 177.92849731445 | wgEncodeYaleChIPseqPeaksHelas3Cfos;
| 1.2226899862289 | 1352.9223632812 | 1.3019100427628 | 260.36569213867 | 1.8232300281525 | 265.30029296875 | wgEncodeYaleChIPseqPeaksHelas3Cmyc;
| 1.1304099559784 | 733.25946044922 | 1.3024799823761 | 283.87057495117 | 1.8091399669647 | 288.8776550293 | wgEncodeYaleChIPseqPeaksHelas3Max;
| 1.1479400396347 | 1420.5920410156 | 1.303789973259 | 222.53610229492 | 1.4720799922943 | 226.95211791992 | wgEncodeYaleChIPseqPeaksK562Rad21;
| 1.2304999828339 | 446.61828613281 | 1.3087400197983 | 207.92915344238 | 2.5831201076508 | 211.45474243164 | wgEncodeYaleChIPseqPeaksK562Xrcc4;
| 1.331200003624 | 2248.4096679688 | 1.301059961319 | 300 | 1.9688999652863 | 300 | wgEncodeYaleChIPseqRel2PeaksGm12878Cfos;
| 1.2527199983597 | 7042.3569335938 | 1.3050899505615 | 96.54231262207 | 1.5731699466705 | 300 | wgEncodeYaleChIPseqRel2PeaksGm12878Jund;
| 1.1049200296402 | 2727.3859863281 | 1.3020499944687 | 85.993377685547 | 2.049770116806 | 90.847427368164 | wgEncodeYaleChIPseqRel2PeaksGm12878Max;
| 1.2164100408554 | 1979.5601806641 | 1.3021899461746 | 300 | 1.8839600086212 | 300 | wgEncodeYaleChIPseqRel2PeaksGm12878Pol2;
| 1.1837500333786 | 2858.4267578125 | 1.302060008049 | 300 | 1.4207600355148 | 300 | wgEncodeYaleChIPseqRel2PeaksHct116Tcf4;
| 1.3379199504852 | 1814.4339599609 | 1.3035399913788 | 300 | 1.6756000518799 | 300 | wgEncodeYaleChIPseqRel2PeaksHek293Pol2;
| -0.3072899878025 | 1137.6721191406 | 1.301059961319 | 231.30393981934 | 1.7342599630356 | 233.51809692383 | wgEncodeYaleChIPseqRel2PeaksHelas3Pol2;
| 1.1689599752426 | 872.79962158203 | 1.3033900260925 | 300 | 1.7389299869537 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Cfos;
| 1.1969499588013 | 327.81936645508 | 1.3026900291443 | 229.9097442627 | 1.7244700193405 | 234.90943908691 | wgEncodeYaleChIPseqRel2PeaksK562Cjun;
| 1.2487000226974 | 203.55351257324 | 1.3012200593948 | 257.67834472656 | 1.8194299936295 | 262.02362060547 | wgEncodeYaleChIPseqRel2PeaksK562Cmyc;
| 1.0990400314331 | 18241.177734375 | 1.3014600276947 | 160.30415344238 | 1.4422600269318 | 164.9938659668 | wgEncodeYaleChIPseqRel2PeaksK562Gata1;
| 1.181480050087 | 47.822288513184 | 1.3025200366974 | 240.95959472656 | 2.1446800231934 | 245.24108886719 | wgEncodeYaleChIPseqRel2PeaksK562Jund;
| 1.2188500165939 | 133.69340515137 | 1.3030099868774 | 213.0196685791 | 1.827919960022 | 217.79626464844 | wgEncodeYaleChIPseqRel2PeaksK562Max;
| 1.2230999469757 | 77.342399597168 | 1.3015500307083 | 297.89761352539 | 1.8038400411606 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Nfe2;
| 1.1640499830246 | 2476.1047363281 | 1.303200006485 | 300 | 1.7722599506378 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Pol2;
| 1.170009970665 | 10674.33203125 | 1.3010300397873 | 300 | 1.6494699716568 | 300 | wgEncodeYaleChIPseqRel2PeaksK562Znf263;
| 1.2452100515366 | 3450.4016113281 | 1.3032200336456 | 300 | 1.5723099708557 | 300 | wgEncodeYaleChIPseqRel2PeaksNb4Pol2;
Ignore negative signalValue
1 18241 1 300 1 300
# Yale asks to exclude chrM which has the negative values:
select * from wgEncodeYaleChIPseqRel2PeaksHelas3Pol2 where signalValue < 0;
+-----+-------+------------+----------+------+-------+--------+-------------+---------+---------+------+
| bin | chrom | chromStart | chromEnd | name | score | strand | signalValue | pValue | qValue | peak |
+-----+-------+------------+----------+------+-------+--------+-------------+---------+---------+------+
| 585 | chrM | 0 | 1030 | . | 1000 | . | -0.26456 | 231.304 | 233.518 | 140 |
| 585 | chrM | 1261 | 4108 | . | 1000 | . | -0.28738 | 231.304 | 233.518 | 2012 |
| 585 | chrM | 4780 | 5491 | . | 1000 | . | -0.22651 | 231.304 | 233.518 | 195 |
| 585 | chrM | 5832 | 5857 | . | 1000 | . | -0.27361 | 231.304 | 233.518 | 18 |
| 585 | chrM | 6228 | 6648 | . | 1000 | . | -0.22728 | 231.304 | 233.518 | 170 |
| 585 | chrM | 6927 | 7204 | . | 1000 | . | -0.27805 | 231.304 | 233.518 | 101 |
| 585 | chrM | 7691 | 16659 | . | 1000 | . | -0.30729 | 231.304 | 233.518 | 8474 |
+-----+-------+------------+----------+------+-------+--------+-------------+---------+---------+------+
7 rows in set (0.02 sec)
delete from wgEncodeYaleChIPseqRel2PeaksHelas3Pol2 where chrom = "chrM";
Query OK, 7 rows affected (0.00 sec)
select min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeYaleChIPseqRel2PeaksHelas3Pol2;
| 1.210970044136 | 1137.6721191406 | 1.301059961319 | 231.30393981934 | 1.7342599630356 | 233.51809692383 | wgEncodeYaleChIPseqRel2PeaksHelas3Pol2;
# Mark all from this latest drop as displayed:
/cluster/data/encode/pipeline/bin/encodeStatus.pl 315 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 316 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 317 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 318 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 319 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 320 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 323 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 324 displayed
# From Nightly build (all are bedGraph)
hg18.wgEncodeYaleChIPseqRel2SignalGm12878Cfos has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalGm12878Cfos has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalGm12878Jund has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalGm12878Max has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalGm12878Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalGm12878Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalHct116Tcf4 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalHct116Tcf4 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalHek293Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalHelas3Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Cfos has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Gata1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Gata1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Gata1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Gata1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Gata1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Jund has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Max has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Max has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Max has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Znf263 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalK562Znf263 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqRel2SignalNb4Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Cfos has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Max has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Max has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Rad21 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Rad21 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Rad21 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Rad21 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Xrcc4 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Xrcc4 has 1 records with end > chromSize.
# From out/*.err
wgEncodeYaleChIPseqRel2SignalGm12878Cfos
WARNING: Exceeded chr15 size 100338948 > 100338915. dropping 34 data point(s)
WARNING: Exceeded chr18 size 76117313 > 76117153. dropping 161 data point(s)
wgEncodeYaleChIPseqRel2SignalGm12878Jund
WARNING: Exceeded chr10 size 135374860 > 135374737. dropping 124 data point(s)
wgEncodeYaleChIPseqRel2SignalGm12878Max
WARNING: Exceeded chr10 size 135374834 > 135374737. dropping 98 data point(s)
wgEncodeYaleChIPseqRel2SignalGm12878Pol2
WARNING: Exceeded chr10 size 135374835 > 135374737. dropping 99 data point(s)
WARNING: Exceeded chr21 size 46944339 > 46944323. dropping 17 data point(s)
WARNING: Exceeded chr21 size 46944345 > 46944323. dropping 23 data point(s)
wgEncodeYaleChIPseqRel2SignalHct116Tcf4
WARNING: Exceeded chr10 size 135374833 > 135374737. dropping 97 data point(s)
WARNING: Exceeded chr18 size 76117310 > 76117153. dropping 158 data point(s)
wgEncodeYaleChIPseqRel2SignalHek293Pol2
WARNING: Exceeded chr18 size 76117298 > 76117153. dropping 146 data point(s)
wgEncodeYaleChIPseqRel2SignalHelas3Pol2
WARNING: Exceeded chr20 size 62435966 > 62435964. dropping 3 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Cfos
WARNING: Exceeded chr21 size 46944337 > 46944323. dropping 15 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Cjun
WARNING: Exceeded chr10 size 135374802 > 135374737. dropping 66 data point(s)
WARNING: Exceeded chr15 size 100338931 > 100338915. dropping 17 data point(s)
WARNING: Exceeded chr15 size 100338949 > 100338915. dropping 35 data point(s)
WARNING: Exceeded chr18 size 76117290 > 76117153. dropping 138 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Cmyc
WARNING: Exceeded chr7 size 158821445 > 158821424. dropping 22 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Gata1
WARNING: Exceeded chr10 size 135374830 > 135374737. dropping 94 data point(s)
WARNING: Exceeded chr15 size 100338936 > 100338915. dropping 22 data point(s)
WARNING: Exceeded chr20 size 62436027 > 62435964. dropping 64 data point(s)
WARNING: Exceeded chr21 size 46944386 > 46944323. dropping 64 data point(s)
WARNING: Exceeded chr7 size 158821498 > 158821424. dropping 75 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Jund
WARNING: Exceeded chr21 size 46944342 > 46944323. dropping 20 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Max
WARNING: Exceeded chr10 size 135374858 > 135374737. dropping 122 data point(s)
WARNING: Exceeded chr21 size 46944337 > 46944323. dropping 15 data point(s)
WARNING: Exceeded chr7 size 158821485 > 158821424. dropping 62 data point(s)
wgEncodeYaleChIPseqRel2SignalK562Znf263
WARNING: Exceeded chr21 size 46944344 > 46944323. dropping 22 data point(s)
WARNING: Exceeded chr7 size 158821426 > 158821424. dropping 3 data point(s)
wgEncodeYaleChIPseqRel2SignalNb4Pol2
WARNING: Exceeded chr7 size 158821447 > 158821424. dropping 24 data point(s)
wgEncodeYaleChIPseqSignalHelas3Cfos
WARNING: Exceeded chr21 size 46944351 > 46944323. dropping 29 data point(s)
wgEncodeYaleChIPseqSignalHelas3Cmyc
WARNING: Exceeded chr10 size 135374834 > 135374737. dropping 98 data point(s)
WARNING: Exceeded chr18 size 76117311 > 76117153. dropping 159 data point(s)
WARNING: Exceeded chr21 size 46944338 > 46944323. dropping 16 data point(s)
wgEncodeYaleChIPseqSignalHelas3Max
WARNING: Exceeded chr21 size 46944356 > 46944323. dropping 34 data point(s)
WARNING: Exceeded chr7 size 158821487 > 158821424. dropping 64 data point(s)
wgEncodeYaleChIPseqSignalK562Rad21
WARNING: Exceeded chr10 size 135374857 > 135374737. dropping 121 data point(s)
WARNING: Exceeded chr21 size 46944341 > 46944323. dropping 19 data point(s)
WARNING: Exceeded chr7 size 158821451 > 158821424. dropping 28 data point(s)
WARNING: Exceeded chr8 size 146274839 > 146274826. dropping 14 data point(s)
WARNING: Exceeded chr8 size 146274850 > 146274826. dropping 25 data point(s)
wgEncodeYaleChIPseqSignalK562Xrcc4
WARNING: Exceeded chr10 size 135374857 > 135374737. dropping 121 data point(s)
WARNING: Exceeded chr21 size 46944337 > 46944323. dropping 15 data point(s)
select count(*) from wgEncodeYaleChIPseqRel2SignalGm12878Cfos where chrom = "chr15" and chromEnd > 100338915;
select count(*) from wgEncodeYaleChIPseqRel2SignalGm12878Cfos where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqRel2SignalGm12878Jund where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalGm12878Max where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalGm12878Pol2 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalGm12878Pol2 where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqRel2SignalHct116Tcf4 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalHct116Tcf4 where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqRel2SignalHek293Pol2 where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqRel2SignalHelas3Pol2 where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Cfos where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Cjun where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Cjun where chrom = "chr15" and chromEnd > 100338915;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Cjun where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Cmyc where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Gata1 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Gata1 where chrom = "chr15" and chromEnd > 100338915;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Gata1 where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Gata1 where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Gata1 where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Jund where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Max where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Max where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Max where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Znf263 where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqRel2SignalK562Znf263 where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqRel2SignalNb4Pol2 where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqSignalHelas3Cfos where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqSignalHelas3Cmyc where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqSignalHelas3Cmyc where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqSignalHelas3Cmyc where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqSignalHelas3Max where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqSignalHelas3Max where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqSignalK562Rad21 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqSignalK562Rad21 where chrom = "chr21" and chromEnd > 46944323;
select count(*) from wgEncodeYaleChIPseqSignalK562Rad21 where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqSignalK562Rad21 where chrom = "chr8" and chromEnd > 146274826;
select count(*) from wgEncodeYaleChIPseqSignalK562Xrcc4 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqSignalK562Xrcc4 where chrom = "chr21" and chromEnd > 46944323;
All return:
+----------+
| count(*) |
+----------+
| 1 |
+----------+
update wgEncodeYaleChIPseqRel2SignalGm12878Cfos set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqRel2SignalGm12878Cfos set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
update wgEncodeYaleChIPseqRel2SignalGm12878Jund set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalGm12878Max set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalGm12878Pol2 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalGm12878Pol2 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqRel2SignalHct116Tcf4 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalHct116Tcf4 set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
update wgEncodeYaleChIPseqRel2SignalHek293Pol2 set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
update wgEncodeYaleChIPseqRel2SignalHelas3Pol2 set chromEnd = 62435964 where chrom = "chr20" and chromEnd > 62435964 ;
update wgEncodeYaleChIPseqRel2SignalK562Cfos set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqRel2SignalK562Cjun set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalK562Cjun set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqRel2SignalK562Cjun set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
update wgEncodeYaleChIPseqRel2SignalK562Cmyc set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqRel2SignalK562Gata1 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalK562Gata1 set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqRel2SignalK562Gata1 set chromEnd = 62435964 where chrom = "chr20" and chromEnd > 62435964 ;
update wgEncodeYaleChIPseqRel2SignalK562Gata1 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqRel2SignalK562Gata1 set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqRel2SignalK562Jund set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqRel2SignalK562Max set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqRel2SignalK562Max set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqRel2SignalK562Max set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqRel2SignalK562Znf263 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqRel2SignalK562Znf263 set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqRel2SignalNb4Pol2 set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalHelas3Cfos set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqSignalHelas3Cmyc set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalHelas3Cmyc set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
update wgEncodeYaleChIPseqSignalHelas3Cmyc set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqSignalHelas3Max set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqSignalHelas3Max set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalK562Rad21 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalK562Rad21 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
update wgEncodeYaleChIPseqSignalK562Rad21 set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalK562Rad21 set chromEnd = 146274826 where chrom = "chr8" and chromEnd > 146274826;
update wgEncodeYaleChIPseqSignalK562Xrcc4 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalK562Xrcc4 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
# All done with that!
Regenerate RawSignals accidentally generated at fragLength=700 2009-05-07
=========================================================================
# Created 3 DAF/DDF pairs:
rawSigYale.D*F
rawSigYaleInput.D*F
rawSigYaleRna.D*F
# prepare archives and submit them
tar -cpzf rawSigYale.tgz rawSigYale.D*F
tar -cpzf rawSigYaleInput.tgz rawSigYaleInput.D*F
tar -cpzf rawSigYaleRna.tgz rawSigYaleRna.D*F
rename table wgEncodeYaleChIPseqRawSignalHek293Input to wgEncodeYaleChIPseqRawSignalHek293Input_700;
rename table wgEncodeYaleChIPseqRawSignalHct116Input to wgEncodeYaleChIPseqRawSignalHct116Input_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Hepg2Input to wgEncodeYaleChIPseqRawSignalRep1Hepg2Input_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Hepg2Input to wgEncodeYaleChIPseqRawSignalRep2Hepg2Input_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Hepg2Input to wgEncodeYaleChIPseqRawSignalRep3Hepg2Input_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Gm12878Cfos to wgEncodeYaleChIPseqRawSignalRep1Gm12878Cfos_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Gm12878Cfos to wgEncodeYaleChIPseqRawSignalRep2Gm12878Cfos_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Gm12878Cfos to wgEncodeYaleChIPseqRawSignalRep3Gm12878Cfos_700;
rename table wgEncodeYaleChIPseqRawSignalRep1K562Nfe2 to wgEncodeYaleChIPseqRawSignalRep1K562Nfe2_700;
rename table wgEncodeYaleChIPseqRawSignalRep2K562Nfe2 to wgEncodeYaleChIPseqRawSignalRep2K562Nfe2_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Gm12878Max to wgEncodeYaleChIPseqRawSignalRep1Gm12878Max_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Gm12878Max to wgEncodeYaleChIPseqRawSignalRep2Gm12878Max_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Hek293Pol2 to wgEncodeYaleChIPseqRawSignalRep1Hek293Pol2_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Hek293Pol2 to wgEncodeYaleChIPseqRawSignalRep2Hek293Pol2_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Hek293Pol2 to wgEncodeYaleChIPseqRawSignalRep3Hek293Pol2_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Helas3Largefragment to wgEncodeYaleChIPseqRawSignalRep1Helas3Largefragment_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Helas3Largefragment to wgEncodeYaleChIPseqRawSignalRep2Helas3Largefragment_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Helas3Mnase to wgEncodeYaleChIPseqRawSignalRep1Helas3Mnase_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Helas3Mnase to wgEncodeYaleChIPseqRawSignalRep2Helas3Mnase_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Helas3Mouseigg to wgEncodeYaleChIPseqRawSignalRep1Helas3Mouseigg_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Helas3Mouseigg to wgEncodeYaleChIPseqRawSignalRep2Helas3Mouseigg_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Helas3Nakeddna to wgEncodeYaleChIPseqRawSignalRep1Helas3Nakeddna_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Helas3Nakeddna to wgEncodeYaleChIPseqRawSignalRep2Helas3Nakeddna_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Helas3Nakeddna to wgEncodeYaleChIPseqRawSignalRep3Helas3Nakeddna_700;
rename table wgEncodeYaleChIPseqRawSignalRep1K562Znf263 to wgEncodeYaleChIPseqRawSignalRep1K562Znf263_700;
rename table wgEncodeYaleChIPseqRawSignalRep2K562Znf263 to wgEncodeYaleChIPseqRawSignalRep2K562Znf263_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Hct116Tcf4 to wgEncodeYaleChIPseqRawSignalRep1Hct116Tcf4_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Hct116Tcf4 to wgEncodeYaleChIPseqRawSignalRep2Hct116Tcf4_700;
rename table wgEncodeYaleChIPseqRawSignalRep1K562Max to wgEncodeYaleChIPseqRawSignalRep1K562Max_700;
rename table wgEncodeYaleChIPseqRawSignalRep2K562Max to wgEncodeYaleChIPseqRawSignalRep2K562Max_700;
rename table wgEncodeYaleChIPseqRawSignalRep1K562Gata1 to wgEncodeYaleChIPseqRawSignalRep1K562Gata1_700;
rename table wgEncodeYaleChIPseqRawSignalRep2K562Gata1 to wgEncodeYaleChIPseqRawSignalRep2K562Gata1_700;
rename table wgEncodeYaleChIPseqRawSignalRep1K562Jund to wgEncodeYaleChIPseqRawSignalRep1K562Jund_700;
rename table wgEncodeYaleChIPseqRawSignalRep2K562Jund to wgEncodeYaleChIPseqRawSignalRep2K562Jund_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Gm12878Jund to wgEncodeYaleChIPseqRawSignalRep1Gm12878Jund_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Gm12878Jund to wgEncodeYaleChIPseqRawSignalRep2Gm12878Jund_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Hepg2Pol2 to wgEncodeYaleChIPseqRawSignalRep1Hepg2Pol2_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Hepg2Pol2 to wgEncodeYaleChIPseqRawSignalRep2Hepg2Pol2_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Hepg2Pol2 to wgEncodeYaleChIPseqRawSignalRep3Hepg2Pol2_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Hepg2Srebp1a to wgEncodeYaleChIPseqRawSignalRep1Hepg2Srebp1a_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Hepg2Srebp1a to wgEncodeYaleChIPseqRawSignalRep2Hepg2Srebp1a_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Hepg2Srebp1a to wgEncodeYaleChIPseqRawSignalRep3Hepg2Srebp1a_700;
rename table wgEncodeYaleChIPseqRawSignalRep1Hepg2Srebp2 to wgEncodeYaleChIPseqRawSignalRep1Hepg2Srebp2_700;
rename table wgEncodeYaleChIPseqRawSignalRep2Hepg2Srebp2 to wgEncodeYaleChIPseqRawSignalRep2Hepg2Srebp2_700;
rename table wgEncodeYaleChIPseqRawSignalRep3Hepg2Srebp2 to wgEncodeYaleChIPseqRawSignalRep3Hepg2Srebp2_700;
rename table wgEncodeYaleRnaSeqPolyaRawSignalK562 to wgEncodeYaleRnaSeqPolyaRawSignalK562_200;
### Ouch! Can't proceed because these tracks are released. Must do a rel2 version: reedit DAFs and submit
This is not the case for Rna PolyA. Just replace the table:
| wgEncodeYaleRnaSeqPolyaRawSignalK562 |
| wgEncodeYaleRnaSeqPolyaRel2RawSignalK562 |
rename table wgEncodeYaleRnaSeqPolyaRawSignalK562 to wgEncodeYaleRnaSeqPolyaRawSignalK562_200;
rename table wgEncodeYaleRnaSeqPolyaRel2RawSignalK562 to wgEncodeYaleRnaSeqPolyaRawSignalK562;
# Edited trackDb.wgEncode.ra to add all of these, leaving the old tracks ae 'releasse beta'.
/cluster/data/encode/pipeline/bin/encodeStatus.pl 329 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 330 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 331 displayed
Rename the bedGraph tables to be consistent with the more recently resubmitted tables:
| wgEncodeYaleChIPseqSignalGm12878InputBg |
| wgEncodeYaleChIPseqSignalHct116InputBg |
| wgEncodeYaleChIPseqSignalHek293InputBg |
| wgEncodeYaleChIPseqSignalHelas3InputBg |
| wgEncodeYaleChIPseqSignalHelas3ifngInputBg |
| wgEncodeYaleChIPseqSignalHepg2InputBg |
| wgEncodeYaleChIPseqSignalK562InputBg |
| wgEncodeYaleChIPseqSignalNb4InputBg |
select tableName,type from trackDb_tdreszer where tableName = "wgEncodeYaleChIPseqSignalGm12878InputBg";
+-----------------------------------------+------------+
| tableName | type |
+-----------------------------------------+------------+
| wgEncodeYaleChIPseqSignalGm12878InputBg | bedGraph 4 |
The new stype is "wgEncodeYaleChIPseqRel2" so
| wgEncodeYaleChIPseqRel2SignalK562Pol2 | bedGraph 4 |
rename table wgEncodeYaleChIPseqSignalGm12878InputBg to wgEncodeYaleChIPseqRel2SignalGm12878Input ;
rename table wgEncodeYaleChIPseqSignalHct116InputBg to wgEncodeYaleChIPseqRel2SignalHct116Input ;
rename table wgEncodeYaleChIPseqSignalHek293InputBg to wgEncodeYaleChIPseqRel2SignalHek293Input ;
rename table wgEncodeYaleChIPseqSignalHelas3InputBg to wgEncodeYaleChIPseqRel2SignalHelas3Input ;
rename table wgEncodeYaleChIPseqSignalHelas3ifngInputBg to wgEncodeYaleChIPseqRel2SignalHelas3ifngInput;
rename table wgEncodeYaleChIPseqSignalHepg2InputBg to wgEncodeYaleChIPseqRel2SignalHepg2Input ;
rename table wgEncodeYaleChIPseqSignalK562InputBg to wgEncodeYaleChIPseqRel2SignalK562Input ;
rename table wgEncodeYaleChIPseqSignalNb4InputBg to wgEncodeYaleChIPseqRel2SignalNb4Input ;
Latest 2009-5-16
================
# subIds: 333,334
# 333 went in smoothely but nightly chron job:
hg18.wgEncodeYaleChIPseqSignalHct116Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHct116Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHct116Pol2 has 1 records with end > chromSize.
select t1.chrom,t1.chromEnd from wgEncodeYaleChIPseqSignalHct116Pol2 t1,chromInfo t2 where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
update wgEncodeYaleChIPseqSignalHct116Pol2 set chromEnd = 135374737 where chrom = "chr10" and chromEnd = 135374848;
update wgEncodeYaleChIPseqSignalHct116Pol2 set chromEnd = 100338915 where chrom = "chr15" and chromEnd = 100338947;
update wgEncodeYaleChIPseqSignalHct116Pol2 set chromEnd = 46944323 where chrom = "chr21" and chromEnd = 46944379;
# 334
m validation error:
ERROR: failed validateTagAlign : Error [file=Data/YDH_K562_E2F4_tagAlign_rep1_laneB_FC20891AAXX_2_s_5.bed, line=241926]: end(16572) > chromSize(chrM=16571) [chrM 16537 16572 CCCACACGTTCCCCTTAAATACGACATCAC
GATGG 250 +]
Error [file=Data/YDH_K562_E2F4_tagAlign_rep1_laneB_FC20891AAXX_2_s_5.bed, line=344184]: end(16572) > chromSize(chrM=16571) [chrM 16537 16572 CCCACACGTTCCCCTTAAATAAGACATCACGATGG 1000 +]
Aborting ... found 2 errors in total
### On hold until the 2 K562s and the 2 HepG2s are worked out!
# Farnham has separate inputs for the same cell line. But where are they different and when do we need a new cell line?
Need to regenerate Large-Fragment (fragLength=575) 2009-05-22
=============================================================
tar -cpzf rawSigYaleLarge.tgz rawSigYale.DAF rawSigYaleLarge.DDF
show tables like "wgEncodeYale%Rel2RawSignal%Large%";
rename table wgEncodeYaleChIPseqRel2RawSignalRep1Helas3Largefragment to wgEncodeYaleChIPseqRel2RawSignalRep1Helas3Largefragment_old;
rename table wgEncodeYaleChIPseqRel2RawSignalRep2Helas3Largefragment to wgEncodeYaleChIPseqRel2RawSignalRep2Helas3Largefragment_old;
delete from trackDb where tableName = "wgEncodeYaleChIPseqRel2RawSignalRep1Helas3Largefragment";
delete from trackDb where tableName = "wgEncodeYaleChIPseqRel2RawSignalRep2Helas3Largefragment";
drop table wgEncodeYaleChIPseqRel2RawSignalRep1Helas3Largefragment_old;
drop table wgEncodeYaleChIPseqRel2RawSignalRep2Helas3Largefragment_old;
/cluster/data/encode/pipeline/bin/encodeStatus.pl 343 displayed
Generate RawSignal files for download 2009-5-28
===============================================
from pip
grep RawSignal 329/out/load.ra | grep auto >> 325/out/mkRawSigsFiles.sh
grep RawSignal 329/out/load.ra | grep wgEncode >> 325/out/mkRawSigsFiles.sh
...
Edit and then run 329/out/mkRawSigsFiles.sh
placing *.wig.gz into downloads/wgEncodeYaleChIPseq/raw
cd downloads/wgEncodeYaleChIPseq/raw
cp ../preamble.html
cp ../fileDb.ra
edit preamble.html to note the subdirectory only contains Raw Signals
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x ../349 > validate_error 2>&1
Catch up with HCT-116 and add NT2-D1 2009-06-08
===============================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 333 displayed
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 348 displayed
To be done:
/cluster/data/encode/pipeline/bin/encodeStatus.pl 349 displayed
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# Mike Wilson provided this list of datasets that belong to Yale or UCDavis.
# Since K562 and HepG2 have separate inputs for Yale and UCDavis, these two cell lines must be broken down into
# K562/K562b and HepG2/HepG2b (the 'b' version is UCDavis, sorry Peggy)
YHD_NB4_Pol2 Yale
YHD_NB4_Input Yale
YHD_K562_PolyA_RNA Yale
YHD_K562_Pol2 Yale
YHD_K562_NF-E2 Yale
YHD_K562_Myc Yale
YHD_K562_Max Yale
YHD_K562_JunD Yale
YHD_K562_Jun Yale
YHD_K562_Input Yale
YHD_K562_Fos Yale
YHD_HepG2_SREBP2 Yale
YHD_HepG2_SREBP1A Yale
YHD_HepG2_Pol2 Yale
YHD_HepG2_Input Yale
YHD_HeLa-S3_Pol2 Yale
YHD_HeLa-S3_Naked_DNA_Control Yale
YHD_HeLa-S3_MouseIgG_Control Yale
YHD_HeLa-S3_MNase_Control Yale
YHD_HeLa-S3_Large_Fragment_Control Yale
YHD_HeLa-S3_Input Yale
YHD_HeLa-S3_IFNg_STAT1 Yale
YHD_HeLa-S3_IFNg_Input Yale
YHD_HEK293_Pol2 Yale
YHD_HEK293_Input Yale
YHD_GM12878_Pol2 Yale
YHD_GM12878_Max Yale
YHD_GM12878_JunD Yale
YHD_GM12878_Input Yale
YHD_GM12878_c-Fos Yale
YDH_K562_XRCC4 Yale
YDH_K562_Rad21 Yale
YDH_K562-IFNg6h_Pol2 Yale
YDH_K562-IFNg6h_Myc Yale
YDH_K562-IFNg6h_Jun Yale
YDH_K562-IFNg6h_Input Yale
YDH_K562-IFNg30_Input Yale
YDH_K562-IFNa6h_STAT2 Yale
YDH_K562-IFNa6h_STAT1 Yale
YDH_K562-IFNa6h_Pol2 Yale
YDH_K562-IFNa6h_Myc Yale
YDH_K562-IFNa6h_Jun Yale
YDH_K562-IFNa6h_Input Yale
YDH_K562-IFNa30_STAT2 Yale
YDH_K562-IFNa30_STAT1 Yale
YDH_K562-IFNa30_Pol2 Yale
YDH_K562-IFNa30_Myc Yale
YDH_K562-IFNa30_Jun Yale
YDH_K562-IFNa30_Input Yale
YDH_HeLa-S3_Myc Yale
YDH_HeLa-S3_Max Yale
YDH_HeLa-S3_c-Fos Yale
YDH_GM12878_Pol3 Yale
YDH_K562_E2F4 UCD
YDH_K562_E2F6 UCD
YHD_K562_GATA-1 UCD
YHD_K562_ZNF263 UCD
YDH_K562_Farnham_Input UCD
YDH_HCT-116_Pol2 UCD
YHD_HCT-116_TCF4 UCD
YHD_HCT-116_Input UCD
YDH_NT2-D1_YY1 UCD
YDH_NT2-D1_SUZ12 UCD
YDH_NT2-D1_Input UCD
YDH_HepG2b_TR4 UCD
YDH_HepG2b_Input UCD
# Of these the following have been submitted but really need to be renamed for the b version:
# NOTE that they are all Rel2 which saves some worry over alpha/beta versions
rename table wgEncodeYaleChIPseqRel2PeaksK562Gata1 to wgEncodeYaleChIPseqRel2PeaksK562bGata1;
rename table wgEncodeYaleChIPseqRel2SignalK562Gata1 to wgEncodeYaleChIPseqRel2SignalK562bGata1;
rename table wgEncodeYaleChIPseqRel2RawSignalRep1K562Gata1 to wgEncodeYaleChIPseqRel2RawSignalRep1K562bGata1;
rename table wgEncodeYaleChIPseqRel2RawSignalRep2K562Gata1 to wgEncodeYaleChIPseqRel2RawSignalRep2K562bGata1;
rename table wgEncodeYaleChIPseqRel2PeaksK562Znf263 to wgEncodeYaleChIPseqRel2PeaksK562bZnf263;
rename table wgEncodeYaleChIPseqRel2SignalK562Znf263 to wgEncodeYaleChIPseqRel2SignalK562bZnf263;
rename table wgEncodeYaleChIPseqRel2RawSignalRep1K562Znf263 to wgEncodeYaleChIPseqRel2RawSignalRep1K562bZnf263;
rename table wgEncodeYaleChIPseqRel2RawSignalRep2K562Znf263 to wgEncodeYaleChIPseqRel2RawSignalRep2K562bZnf263;
cd /gbdb/hg18/wib/
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/329/wgEncodeYaleChIPseqRel2RawSignalRep1K562Gata1.wib wgEncodeYaleChIPseqRel2RawSignalRep1K562bGata1.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/329/wgEncodeYaleChIPseqRel2RawSignalRep2K562Gata1.wib wgEncodeYaleChIPseqRel2RawSignalRep2K562bGata1.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/329/wgEncodeYaleChIPseqRel2RawSignalRep1K562Znf263.wib wgEncodeYaleChIPseqRel2RawSignalRep1K562bZnf263.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/329/wgEncodeYaleChIPseqRel2RawSignalRep2K562Znf263.wib wgEncodeYaleChIPseqRel2RawSignalRep2K562bZnf263.wib
update wgEncodeYaleChIPseqRel2RawSignalRep1K562bGata1 set file = "/gbdb/hg18/wib/wgEncodeYaleChIPseqRel2RawSignalRep1K562bGata1.wib";
update wgEncodeYaleChIPseqRel2RawSignalRep2K562bGata1 set file = "/gbdb/hg18/wib/wgEncodeYaleChIPseqRel2RawSignalRep2K562bGata1.wib";
update wgEncodeYaleChIPseqRel2RawSignalRep1K562bZnf263 set file = "/gbdb/hg18/wib/wgEncodeYaleChIPseqRel2RawSignalRep1K562bZnf263.wib";
update wgEncodeYaleChIPseqRel2RawSignalRep2K562bZnf263 set file = "/gbdb/hg18/wib/wgEncodeYaleChIPseqRel2RawSignalRep2K562bZnf263.wib";
rm wgEncodeYaleChIPseqRel2RawSignalRep1K562Gata1.wib
rm wgEncodeYaleChIPseqRel2RawSignalRep2K562Gata1.wib
rm wgEncodeYaleChIPseqRel2RawSignalRep1K562Znf263.wib
rm wgEncodeYaleChIPseqRel2RawSignalRep2K562Znf263.wib
# gold; cd wgEncodeYaleChipSeq
mv wgEncodeYaleChIPseqRel2PeaksK562Gata1.narrowPeak.gz wgEncodeYaleChIPseqRel2PeaksK562bGata1.narrowPeak.gz
mv wgEncodeYaleChIPseqRel2SignalK562Gata1.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalK562bGata1.bedGraph4.gz
mv wgEncodeYaleChIPseqRel2PeaksK562Znf263.narrowPeak.gz wgEncodeYaleChIPseqRel2PeaksK562bZnf263.narrowPeak.gz
mv wgEncodeYaleChIPseqRel2SignalK562Znf263.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalK562bZnf263.bedGraph4.gz
# cd raw
mv wgEncodeYaleChIPseqRel2RawSignalRep1K562Gata1.wig.gz wgEncodeYaleChIPseqRel2RawSignalRep1K562bGata1.wig.gz
mv wgEncodeYaleChIPseqRel2RawSignalRep2K562Gata1.wig.gz wgEncodeYaleChIPseqRel2RawSignalRep2K562bGata1.wig.gz
mv wgEncodeYaleChIPseqRel2RawSignalRep1K562Znf263.wig.gz wgEncodeYaleChIPseqRel2RawSignalRep1K562bZnf263.wig.gz
mv wgEncodeYaleChIPseqRel2RawSignalRep2K562Znf263.wig.gz wgEncodeYaleChIPseqRel2RawSignalRep2K562bZnf263.wig.gz
### Where are the tagAligns? The Rel2 Raw are built from non-Rel2. These need renaming. Files in beta will be renamed in alpha!
mv wgEncodeYaleChIPseqAlignmentsRep1K562Gata1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562bGata1.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2K562Gata1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562bGata1.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1K562Znf263.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562bZnf263.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2K562Znf263.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562bZnf263.tagAlign.gz
Need to patch trackDb.ra nd fileDb.ra for name changes! Therefore, all file names have been changed to the 'b' versions for K562/Gata1 and K562/ZNF263
mv wgEncodeYaleChIPseqSignalGm12878Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalGm12878Input.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHct116Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalHct116Input.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHek293Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalHek293Input.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHelas3Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalHelas3Input.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHelas3ifngInput.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalHelas3ifngInput.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalHepg2Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalHepg2Input.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalK562E2f4.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalK562E2f4.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalK562Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalK562Input.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalNb4Input.bedGraph4.gz wgEncodeYaleChIPseqRel2SignalNb4Input.bedGraph4.gz
/cluster/data/encode/pipeline/bin/encodeStatus.pl 334 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 335 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 372 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 374 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 371 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 377 displayed
Fix nightly chron job output 2009-06-16
=======================================
hg18.wgEncodeYaleChIPseqSignalK562Ifna30Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna30Input has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna6hInput has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng30Input has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng6hInput has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalNt2d1Input has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna30Stat1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna6hCjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna6hCmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna6hStat1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifna6hStat2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng6hCjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng6hCmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng6hPol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2bInput has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2bTr4 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng30Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562bInput has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562bE2f6 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562bSetdb1 has 1 records with end > chromSize.
select t2.size,t1.chrom,t1.chromEnd from wgEncodeYaleChIPseqSignalK562Ifna30Stat1 t1,chromInfo t2 where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
| 158821424 | chr7 | 158821429 |
update wgEncodeYaleChIPseqSignalHepg2bTr4 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 4 Changed: 4 Warnings: 0
update wgEncodeYaleChIPseqSignalHepg2bInput t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 2 Changed: 2 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna30Cmyc t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 4 Changed: 4 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna30Stat1 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 1 Changed: 1 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna30Input t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 4 Changed: 4 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna6hCjun t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 3 Changed: 3 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna6hCmyc t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 2 Changed: 2 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna6hStat1 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 2 Changed: 2 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna6hStat2 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 1 Changed: 1 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifna6hInput t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 4 Changed: 4 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifng30Cjun t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 3 Changed: 3 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifng30Input t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 1 Changed: 1 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifng6hCjun t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 2 Changed: 2 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifng6hCmyc t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 4 Changed: 4 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifng6hPol2 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 2 Changed: 2 Warnings: 0
update wgEncodeYaleChIPseqSignalK562Ifng6hInput t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 3 Changed: 3 Warnings: 0
update wgEncodeYaleChIPseqSignalK562bE2f6 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 3 Changed: 3 Warnings: 0
update wgEncodeYaleChIPseqSignalK562bSetdb1 t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 3 Changed: 3 Warnings: 0
update wgEncodeYaleChIPseqSignalK562bInput t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 4 Changed: 4 Warnings: 0
update wgEncodeYaleChIPseqSignalNt2d1Input t1,chromInfo t2 set t1.chromEnd = t2.size where t1.chrom = t2.chrom and t1.chromEnd > t2.size;
Rows matched: 2 Changed: 2 Warnings: 0
New submissions 2009-06-24
==========================
# Fix my screwup in doEncodeValidate.pl
rename table wgEncodeYaleChIPseqSignalK562bTr4V to wgEncodeYaleChIPseqSignalK562bTr4;
rename table wgEncodeYaleChIPseqPeaksK562bTr4V to wgEncodeYaleChIPseqPeaksK562bTr4;
rename table wgEncodeYaleChIPseqRawSignalRep2K562bTr4V to wgEncodeYaleChIPseqRawSignalRep2K562bTr4;
rename table wgEncodeYaleChIPseqRawSignalRep1K562bTr4V to wgEncodeYaleChIPseqRawSignalRep1K562bTr4;
mv wgEncodeYaleChIPseqAlignmentsRep1K562bTr4V.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562bTr4.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2K562bTr4V.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562bTr4.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksK562bTr4V.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562bTr4.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1K562bTr4V.fastq.gz wgEncodeYaleChIPseqRawDataRep1K562bTr4.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2K562bTr4V.fastq.gz wgEncodeYaleChIPseqRawDataRep2K562bTr4.fastq.gz
mv wgEncodeYaleChIPseqSignalK562bTr4V.bedGraph4.gz wgEncodeYaleChIPseqSignalK562bTr4.bedGraph4.gz
mv wgEncodeYaleChIPseqRawSignalRep1K562bTr4V.wib wgEncodeYaleChIPseqRawSignalRep1K562bTr4.wib
mv wgEncodeYaleChIPseqRawSignalRep2K562bTr4V.wib wgEncodeYaleChIPseqRawSignalRep2K562bTr4.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/380/wgEncodeYaleChIPseqRawSignalRep1K562bTr4.wib /gbdb/hg18/wib/wgEncodeYaleChIPseqRawSignalRep1K562bTr4.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/380/wgEncodeYaleChIPseqRawSignalRep2K562bTr4.wib /gbdb/hg18/wib/wgEncodeYaleChIPseqRawSignalRep2K562bTr4.wib
update wgEncodeYaleChIPseqRawSignalRep1K562bTr4 set file = "/gbdb/hg18/wib/wgEncodeYaleChIPseqRawSignalRep1K562bTr4.wib";
update wgEncodeYaleChIPseqRawSignalRep2K562bTr4 set file = "/gbdb/hg18/wib/wgEncodeYaleChIPseqRawSignalRep2K562bTr4.wib";
/cluster/data/encode/pipeline/bin/encodeStatus.pl 380 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 383 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 384 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 385 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 386 displayed
Resubmissions 2009-06-30
==========================
# Unfortunately, Mike submitted with the Rel2 version so:
rename table wgEncodeYaleChIPseqPeaksK562Bdp1 to wgEncodeYaleOldChIPseqPeaksK562Bdp1;
rename table wgEncodeYaleChIPseqPeaksK562Brf1 to wgEncodeYaleOldChIPseqPeaksK562Brf1;
rename table wgEncodeYaleChIPseqPeaksK562Rad21 to wgEncodeYaleOldChIPseqPeaksK562Rad21;
rename table wgEncodeYaleChIPseqPeaksK562Rpc155 to wgEncodeYaleOldChIPseqPeaksK562Rpc155;
rename table wgEncodeYaleChIPseqPeaksK562Sirt6 to wgEncodeYaleOldChIPseqPeaksK562Sirt6;
rename table wgEncodeYaleChIPseqPeaksK562Xrcc4 to wgEncodeYaleOldChIPseqPeaksK562Xrcc4;
rename table wgEncodeYaleChIPseqRel2PeaksK562Bdp1 to wgEncodeYaleChIPseqPeaksK562Bdp1;
rename table wgEncodeYaleChIPseqRel2PeaksK562Brf1 to wgEncodeYaleChIPseqPeaksK562Brf1;
rename table wgEncodeYaleChIPseqRel2PeaksK562Rad21 to wgEncodeYaleChIPseqPeaksK562Rad21;
rename table wgEncodeYaleChIPseqRel2PeaksK562Rpc155 to wgEncodeYaleChIPseqPeaksK562Rpc155;
rename table wgEncodeYaleChIPseqRel2PeaksK562Sirt6 to wgEncodeYaleChIPseqPeaksK562Sirt6;
rename table wgEncodeYaleChIPseqRel2PeaksK562Xrcc4 to wgEncodeYaleChIPseqPeaksK562Xrcc4;
drop table wgEncodeYaleChIPseqPeaksK562Bdp1 ;
drop table wgEncodeYaleChIPseqPeaksK562Brf1 ;
drop table wgEncodeYaleChIPseqPeaksK562Rad21 ;
drop table wgEncodeYaleChIPseqPeaksK562Rpc155;
drop table wgEncodeYaleChIPseqPeaksK562Sirt6 ;
drop table wgEncodeYaleChIPseqPeaksK562Xrcc4 ;
# Oops!!!
doEncodeLoad.pl x ../405 > load_error 2>&1 &
rename table wgEncodeYaleChIPseqRel2PeaksK562Bdp1_405 to wgEncodeYaleChIPseqPeaksK562Bdp1;
rename table wgEncodeYaleChIPseqRel2PeaksK562Brf1_405 to wgEncodeYaleChIPseqPeaksK562Brf1;
rename table wgEncodeYaleChIPseqRel2PeaksK562Rad21_405 to wgEncodeYaleChIPseqPeaksK562Rad21;
rename table wgEncodeYaleChIPseqRel2PeaksK562Rpc155_405 to wgEncodeYaleChIPseqPeaksK562Rpc155;
rename table wgEncodeYaleChIPseqRel2PeaksK562Sirt6_405 to wgEncodeYaleChIPseqPeaksK562Sirt6;
rename table wgEncodeYaleChIPseqRel2PeaksK562Xrcc4_405 to wgEncodeYaleChIPseqPeaksK562Xrcc4;
drop table wgEncodeYaleOldChIPseqPeaksK562Bdp1 ;
drop table wgEncodeYaleOldChIPseqPeaksK562Brf1 ;
drop table wgEncodeYaleOldChIPseqPeaksK562Rad21 ;
drop table wgEncodeYaleOldChIPseqPeaksK562Rpc155;
drop table wgEncodeYaleOldChIPseqPeaksK562Sirt6 ;
drop table wgEncodeYaleOldChIPseqPeaksK562Xrcc4 ;
mv wgEncodeYaleChIPseqPeaksK562Bdp1.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksK562Brf1.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksK562Rad21.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksK562Rpc155.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksK562Sirt6.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksK562Xrcc4.narrowPeak.gz old
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562Bdp1.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Bdp1.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562Brf1.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Brf1.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562Rad21.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Rad21.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562Rpc155.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Rpc155.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562Sirt6.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Sirt6.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562Xrcc4.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Xrcc4.narrowPeak.gz
# Edited a bunch of metadata to standardize on 'submittedDataVersion=V2'
mv wgEncodeYaleChIPseqRel2PeaksGm12878Cfos.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksGm12878Jund.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksGm12878Max.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksGm12878Pol2.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksHct116Tcf4.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksHek293Pol2.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksHelas3Pol2.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Cfos.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Cjun.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Cmyc.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Jund.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Max.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Nfe2.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562Pol2.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562bGata1.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksK562bZnf263.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2PeaksNb4Pol2.narrowPeak.gz old
mv wgEncodeYaleChIPseqRel2SignalK562Input.bedGraph4.gz old
/cluster/data/encode/pipeline/bin/encodeStatus.pl 390 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 404 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 405 displayed
Resubmit more peaks 2009-07-20
==============================
rename table wgEncodeYaleChIPseqRel2PeaksHelas3Max to wgEncodeYaleChIPseqPeaksHelas3MaxV2;
rename table wgEncodeYaleChIPseqRel2PeaksHelas3Cfos to wgEncodeYaleChIPseqPeaksHelas3CfosV2;
rename table wgEncodeYaleChIPseqRel2PeaksHelas3Cmyc to wgEncodeYaleChIPseqPeaksHelas3CmycV2;
rename table wgEncodeYaleChIPseqRel2PeaksHct116Pol2 to wgEncodeYaleChIPseqPeaksHct116Pol2V2;
rename table wgEncodeYaleChIPseqRel2PeaksK562bE2f4 to wgEncodeYaleChIPseqPeaksK562bE2f4V2;
drop table wgEncodeYaleChIPseqRel2PeaksGm12878Pol2;
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksHelas3Max.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3MaxV2.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksHelas3Cfos.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3CfosV2.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksHelas3Cmyc.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3CmycV2.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksHct116Pol2.narrowPeak.gz wgEncodeYaleChIPseqPeaksHct116Pol2V2.narrowPeak.gz
mv ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksK562bE2f4.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562bE2f4V2.narrowPeak.gz
rm ../wgEncodeYaleChIPseqRel2/wgEncodeYaleChIPseqRel2PeaksGm12878Pol2.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksHelas3Max.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksHelas3Cfos.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksHelas3Cmyc.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksHct116Pol2.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksK562bE2f4.narrowPeak.gz old
# Oops. None of these are legitamately V2s
mv wgEncodeYaleChIPseqPeaksHelas3MaxV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3Max.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksHelas3CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3Cfos.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksHelas3CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3Cmyc.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksHct116Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksHct116Pol2.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksK562bE2f4V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562bE2f4.narrowPeak.gz
drop table wgEncodeYaleChIPseqPeaksHelas3Max;
drop table wgEncodeYaleChIPseqPeaksHelas3Cfos;
drop table wgEncodeYaleChIPseqPeaksHelas3Cmyc;
drop table wgEncodeYaleChIPseqPeaksHct116Pol2;
drop table wgEncodeYaleChIPseqPeaksK562bE2f4;
rename table wgEncodeYaleChIPseqPeaksHelas3MaxV2 to wgEncodeYaleChIPseqPeaksHelas3Max;
rename table wgEncodeYaleChIPseqPeaksHelas3CfosV2 to wgEncodeYaleChIPseqPeaksHelas3Cfos;
rename table wgEncodeYaleChIPseqPeaksHelas3CmycV2 to wgEncodeYaleChIPseqPeaksHelas3Cmyc;
rename table wgEncodeYaleChIPseqPeaksHct116Pol2V2 to wgEncodeYaleChIPseqPeaksHct116Pol2;
rename table wgEncodeYaleChIPseqPeaksK562bE2f4V2 to wgEncodeYaleChIPseqPeaksK562bE2f4;
# Edit trackDb.wgEncode.ra for metadata. make DBS=hg18;ci;make alpha DBS=hg18
Now Mike submits using V2 for GM12878/Pol3
drop table wgEncodeYaleChIPseqPeaksGm12878Pol3;
rename table wgEncodeYaleChIPseqPeaksGm12878Pol3V2 to wgEncodeYaleChIPseqPeaksGm12878Pol3;
mv wgEncodeYaleChIPseqPeaksGm12878Pol3.narrowPeak.gz old
mv wgEncodeYaleChIPseqPeaksGm12878Pol3V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol3.narrowPeak.gz
select avg(pValue),avg(qValue) from wgEncodeYaleChIPseqPeaksHelas3Max;
select avg(pValue),avg(qValue) from wgEncodeYaleChIPseqPeaksHelas3Cfos;
select avg(pValue),avg(qValue) from wgEncodeYaleChIPseqPeaksHelas3Cmyc;
select avg(pValue),avg(qValue) from wgEncodeYaleChIPseqPeaksHct116Pol2;
select avg(pValue),avg(qValue) from wgEncodeYaleChIPseqPeaksK562bE2f4;
select avg(pValue),avg(qValue) from wgEncodeYaleChIPseqPeaksGm12878Pol3;
+---------------+-----------------+----------------+
| dataset | avg(pValue) | avg(qValue) |
+---------------+-----------------+----------------+
| HeLa-S3/Max | 12.651372975794 | 11.60438613736 |
| HeLa-S3/c-Fos | 8.4270724793125 | 7.377674166024 |
| HeLa-S3/c-Myc | 10.585949614416 | 9.496844283647 |
| HCT-116/Pol2 | 21.657006559714 | 21.01047205319 |
| K562b/E2f4 | 18.306799526466 | 17.03902673493 |
| GM12878/Pol3 | 14.031863132653 | 11.50519011406 |
+---------------+-----------------+----------------+
/cluster/data/encode/pipeline/bin/encodeStatus.pl 439 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 440 displayed
Resubmitted 8 signals but all are validly V2:
track wgEncodeYaleChIPseqSignalHelas3LargefragmentV2
track wgEncodeYaleChIPseqSignalHelas3MnaseV2
track wgEncodeYaleChIPseqSignalHelas3MouseiggV2
track wgEncodeYaleChIPseqSignalHelas3NakeddnaV2
track wgEncodeYaleChIPseqSignalHepg2Pol2V2
track wgEncodeYaleChIPseqSignalHepg2Srebp1aV2
track wgEncodeYaleChIPseqSignalHepg2Srebp2V2
track wgEncodeYaleChIPseqSignalHelas3ifngStat1V2
# just move the download files around and rebuild
mv wgEncodeYaleChIPseqSignalHelas3Largefragment.wig.gz old
mv wgEncodeYaleChIPseqSignalHelas3Mnase.wig.gz old
mv wgEncodeYaleChIPseqSignalHelas3Mouseigg.wig.gz old
mv wgEncodeYaleChIPseqSignalHelas3Nakeddna.wig.gz old
mv wgEncodeYaleChIPseqSignalHepg2Pol2.wig.gz old
mv wgEncodeYaleChIPseqSignalHepg2Srebp1a.wig.gz old
mv wgEncodeYaleChIPseqSignalHepg2Srebp2.wig.gz old
mv wgEncodeYaleChIPseqSignalHelas3ifngStat1.wig.gz old
/cluster/data/encode/pipeline/bin/encodeStatus.pl 441 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 442 displayed
2009-09-01 A couple more NEW submissions
========================================
Added validationSettings to DAF:
validationSettings validateFiles.tagAlign:mmCheckOneInN=100,mismatches=2
/cluster/data/encode/pipeline/bin/encodeStatus.pl 460 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 467 displayed
Also split RNA-seq PolyA out to its own composite: wgEncodeYaleRNAseq and located it under Expression group
2009-09-24 Three new submissions for Farnham
============================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 536 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 537 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 538 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 539 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 540 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 541 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 542 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 543 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 536 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 537 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 538 approved
2009-10-02 Setting up release1 diectory so that release2 push goes okay
=======================================================================
# Setting up release1 diectory under downloads directory
cd {downloadsDir for Yale ChIP}
mkdir release1
cd release1
# Save RR downloads index.html source as file
# Use it to create master list of downloadable files
# hard link to them from .., ../old or whereever they are found
ln ../wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsHct116Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsHek293Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsHelas3Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsHelas3ifngInput.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsK562Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsNb4Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cfos.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Gm12878Jund.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Gm12878Max.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Hct116Tcf4.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Hek293Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Helas3Largefragment.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Helas3Mnase.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Helas3Mouseigg.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Helas3Nakeddna.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Helas3Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Helas3ifngStat1.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Hepg2Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Hepg2Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Hepg2Srebp1a.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Hepg2Srebp2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Cfos.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Cjun.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Gata1.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Jund.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Max.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Nfe2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562Znf263.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep1Nb4Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cfos.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Gm12878Jund.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Gm12878Max.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Hct116Tcf4.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Hek293Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Helas3Largefragment.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Helas3Mnase.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Helas3Mouseigg.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Helas3Nakeddna.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Helas3Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Helas3ifngStat1.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Hepg2Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Hepg2Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Hepg2Srebp1a.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Hepg2Srebp2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Cfos.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Cjun.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Cmyc.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Gata1.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Jund.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Max.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Nfe2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562Znf263.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep2Nb4Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Gm12878Cfos.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Hek293Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Helas3Nakeddna.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Helas3Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Hepg2Input.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Hepg2Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Hepg2Srebp1a.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Hepg2Srebp2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3K562Cfos.tagAlign.gz .
ln ../wgEncodeYaleChIPseqAlignmentsRep3Nb4Pol2.tagAlign.gz .
ln ../wgEncodeYaleChIPseqPeaksGm12878Cfos.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksGm12878Jund.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksGm12878Max.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksGm12878Pol2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHct116Tcf4.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHek293Pol2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHelas3Largefragment.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHelas3Mouseigg.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHelas3Pol2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHepg2Pol2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHepg2Srebp1a.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksHepg2Srebp2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Cfos.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Cjun.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Cmyc.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Gata1.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Jund.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Max.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Nfe2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Pol2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksK562Znf263.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqPeaksNb4Pol2.narrowPeak.gz .
ln ../wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataHct116Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataHek293Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataHelas3Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataHelas3ifngInput.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataK562Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataNb4Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Gm12878Cfos.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Gm12878Jund.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Gm12878Max.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Gm12878Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Hct116Tcf4.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Hek293Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Helas3Largefragment.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Helas3Mnase.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Helas3Mouseigg.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Helas3Nakeddna.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Helas3Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Helas3ifngStat1.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Hepg2Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Hepg2Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Hepg2Srebp1a.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Hepg2Srebp2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Cfos.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Cjun.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Cmyc.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Gata1.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Jund.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Max.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Nfe2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1K562Znf263.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep1Nb4Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Gm12878Cfos.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Gm12878Jund.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Gm12878Max.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Gm12878Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Hct116Tcf4.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Hek293Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Helas3Largefragment.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Helas3Mnase.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Helas3Mouseigg.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Helas3Nakeddna.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Helas3Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Helas3ifngStat1.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Hepg2Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Hepg2Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Hepg2Srebp1a.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Hepg2Srebp2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Cfos.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Cjun.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Cmyc.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Gata1.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Jund.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Max.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Nfe2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2K562Znf263.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep2Nb4Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Gm12878Cfos.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Hek293Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Helas3Nakeddna.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Helas3Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Hepg2Input.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Hepg2Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Hepg2Srebp1a.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Hepg2Srebp2.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3K562Cfos.fastq.gz .
ln ../wgEncodeYaleChIPseqRawDataRep3Nb4Pol2.fastq.gz .
ln ../wgEncodeYaleChIPseqSignalGm12878Cfos.wig.gz .
ln ../wgEncodeYaleChIPseqSignalGm12878InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalGm12878Jund.wig.gz .
ln ../wgEncodeYaleChIPseqSignalGm12878Max.wig.gz .
ln ../wgEncodeYaleChIPseqSignalGm12878Pol2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHct116InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalHct116Tcf4.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHek293InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalHek293Pol2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3Largefragment.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3Mnase.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3Mouseigg.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3Nakeddna.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3Pol2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3ifngInputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalHelas3ifngStat1.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHepg2InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalHepg2Pol2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHepg2Srebp1a.wig.gz .
ln ../wgEncodeYaleChIPseqSignalHepg2Srebp2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Cfos.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Cjun.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Cmyc.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Gata1.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalK562Jund.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Max.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Nfe2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Pol2.wig.gz .
ln ../wgEncodeYaleChIPseqSignalK562Znf263.wig.gz .
ln ../wgEncodeYaleChIPseqSignalNb4InputBg.bedGraph4.gz .
ln ../wgEncodeYaleChIPseqSignalNb4Pol2.wig.gz .
ln ../wgEncodeYaleRnaSeqPolyaAlignmentsK562.tagAlign.gz .
ln ../wgEncodeYaleRnaSeqPolyaRawDataK562.fastq.gz .
ln ../wgEncodeYaleRnaSeqPolyaSignalK562.bedGraph4.gz .
# Some misses so:
mv ../old/wgEncodeYaleChIPseqPeaksGm12878Cfos.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksGm12878Jund.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksGm12878Max.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksGm12878Pol2.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksHct116Tcf4.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksHek293Pol2.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksHelas3Pol2.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Cfos.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Cjun.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Cmyc.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Gata1.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Jund.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Max.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Nfe2.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Pol2.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksK562Znf263.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqPeaksNb4Pol2.narrowPeak.gz .
mv ../old/wgEncodeYaleChIPseqSignalGm12878Cfos.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalGm12878Jund.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalGm12878Max.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalGm12878Pol2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHct116Tcf4.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHek293Pol2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHelas3Largefragment.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHelas3Mnase.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHelas3Mouseigg.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHelas3Nakeddna.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHelas3Pol2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHelas3ifngStat1.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHepg2Pol2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHepg2Srebp1a.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalHepg2Srebp2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Cfos.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Cjun.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Cmyc.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Gata1.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Jund.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Max.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Nfe2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Pol2.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalK562Znf263.wig.gz .
mv ../old/wgEncodeYaleChIPseqSignalNb4Pol2.wig.gz .
# PolyA is a special case
ls ../../wgEncodeYaleRNAseq/wgEncodeYaleRnaSeqPolyaAlignmentsK562.tagAlign.gz
ls ../../wgEncodeYaleRNAseq/wgEncodeYaleRnaSeqPolyaRawDataK562.fastq.gz
ls ../../wgEncodeYaleRNAseq/wgEncodeYaleRnaSeqPolyaSignalK562.bedGraph4.gz
ln ../../wgEncodeYaleRNAseq/wgEncodeYaleRnaSeqPolyaAlignmentsK562.tagAlign.gz .
ln ../../wgEncodeYaleRNAseq/wgEncodeYaleRnaSeqPolyaRawDataK562.fastq.gz .
ln ../../wgEncodeYaleRNAseq/wgEncodeYaleRnaSeqPolyaSignalK562.bedGraph4.gz .
# Still some misses so investigate
ls ../wgEncodeYaleChIPseqRel2SignalGm12878Input.bedGraph4.gz
ls ../wgEncodeYaleChIPseqRel2SignalHct116Input.bedGraph4.gz
ls ../wgEncodeYaleChIPseqRel2SignalHek293Input.bedGraph4.gz
ls ../wgEncodeYaleChIPseqRel2SignalHelas3Input.bedGraph4.gz
ls ../wgEncodeYaleChIPseqRel2SignalHelas3ifngInput.bedGraph4.gz
ls ../wgEncodeYaleChIPseqRel2SignalHepg2Input.bedGraph4.gz
ls ../wgEncodeYaleChIPseqSignalRep1K562InputV2.bedGraph4.gz
ls ../wgEncodeYaleChIPseqRel2SignalNb4Input.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalGm12878Input.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878InputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalHct116Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHct116InputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalHek293Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHek293InputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalHelas3Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3InputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalHelas3ifngInput.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3ifngInputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalHepg2Input.bedGraph4.gz wgEncodeYaleChIPseqSignalHepg2InputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqSignalRep1K562InputV2.bedGraph4.gz wgEncodeYaleChIPseqSignalK562InputBg.bedGraph4.gz
ln ../wgEncodeYaleChIPseqRel2SignalNb4Input.bedGraph4.gz wgEncodeYaleChIPseqSignalNb4InputBg.bedGraph4.gz
# Still some misses so investigate more
ls ../wgEncodeYaleChIPseqAlignmentsRep1K562bGata1.tagAlign.gz
ls ../wgEncodeYaleChIPseqAlignmentsRep1K562bZnf263.tagAlign.gz
ls ../wgEncodeYaleChIPseqAlignmentsRep2K562bGata1.tagAlign.gz
ls ../wgEncodeYaleChIPseqAlignmentsRep2K562bZnf263.tagAlign.gz
ls ../wgEncodeYaleChIPseqRawDataRep1K562bGata1.fastq.gz
ls ../wgEncodeYaleChIPseqRawDataRep1K562bZnf263.fastq.gz
ls ../wgEncodeYaleChIPseqRawDataRep2K562bGata1.fastq.gz
ls ../wgEncodeYaleChIPseqRawDataRep2K562bZnf263.fastq.gz
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562bGata1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562Gata1.tagAlign.gz
ln ../wgEncodeYaleChIPseqAlignmentsRep1K562bZnf263.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562Znf263.tagAlign.gz
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562bGata1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562Gata1.tagAlign.gz
ln ../wgEncodeYaleChIPseqAlignmentsRep2K562bZnf263.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562Znf263.tagAlign.gz
ln ../wgEncodeYaleChIPseqRawDataRep1K562bGata1.fastq.gz wgEncodeYaleChIPseqRawDataRep1K562Gata1.fastq.gz
ln ../wgEncodeYaleChIPseqRawDataRep1K562bZnf263.fastq.gz wgEncodeYaleChIPseqRawDataRep1K562Znf263.fastq.gz
ln ../wgEncodeYaleChIPseqRawDataRep2K562bGata1.fastq.gz wgEncodeYaleChIPseqRawDataRep2K562Gata1.fastq.gz
ln ../wgEncodeYaleChIPseqRawDataRep2K562bZnf263.fastq.gz wgEncodeYaleChIPseqRawDataRep2K562Znf263.fastq.gz
# All done
2009-10-02 Finishing up Sept 2009 freeze dirs
=============================================
| 553 | YDH_HeLa-S3_HA | loaded |
| 587 | YDH_HeLa-S3_E2F4 | loaded |
| 614 | YDH_K562_NFYA | loaded |
| 615 | YDH_K562_NFYB | loaded |
| 620 | YDH_GM12878_NFKB | loaded |
| 633 | YDH_tagAlign_update_v2 | validate failed |
| 634 | YDH_tagAlign_update | validate failed |
/cluster/data/encode/pipeline/bin/encodeStatus.pl 553 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 587 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 614 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 615 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 620 displayed
2009-10-07 Addressing chrom overrun issues raised by Ann
========================================================
select * from wgEncodeYaleChIPseqPeaksHelas3Pol2V2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
chrM | 7691 | 16659
# Circlular chrM again!!!
select count(*) from wgEncodeYaleChIPseqPeaksHelas3Pol2V2 where chrom = "chrM" and chromEnd = 16659;| 1
delete from wgEncodeYaleChIPseqPeaksHelas3Pol2V2 where chrom = "chrM" and chromEnd = 16659;
Query OK, 1 row affected (0.00 sec)
cd {downloads}/release2
zcat wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz | grep chrM | grep 16659
chrM 7691 16659 . 1000 . -0.30729 231.30394 233.5181 8474
zcat wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz | grep -v chrM > wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak
zcat wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz | grep chrM | grep -v 16659 >> wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak
mv wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz tmp.wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
gzip wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak
ll wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
-rw-rw-r-- 1 tdreszer protein 365615 Oct 7 10:38 wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
ll tmp.wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
-rw-rw-r-- 2 qateam protein 365615 Jun 30 09:48 tmp.wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
cd ..
rm wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
ln release2/wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz .
ll wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
-rw-rw-r-- 2 tdreszer protein 365615 Oct 7 10:38 wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
rm release2/tmp.wgEncodeYaleChIPseqPeaksHelas3Pol2V2.narrowPeak.gz
select y.chrom,y.chromStart,y.chromEnd from wgEncodeYaleChIPseqRel2SignalGm12878Input y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr18 | 76117088 | 76117288 |
select y.chrom,y.chromStart,y.chromEnd from wgEncodeYaleChIPseqRel2SignalHct116Input y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374689 | 135374848 |
| chr15 | 100338745 | 100338933 |
select y.chrom,y.chromStart,y.chromEnd from wgEncodeYaleChIPseqRel2SignalHek293Input y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr21 | 46944293 | 46944346 |
| chr7 | 158821373 | 158821462 |
select y.chrom,y.chromStart,y.chromEnd from wgEncodeYaleChIPseqRel2SignalHelas3ifngInput y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr21 | 46944205 | 46944345 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqRel2SignalHepg2Input y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr15 | 100338748 | 100338948 | 100338915 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3LargefragmentV2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374603 | 135374803 | 135374737 |
| chr18 | 76117011 | 76117211 | 76117153 |
| chr21 | 46944168 | 46944341 | 46944323 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3MnaseV2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr21 | 46944292 | 46944378 | 46944323 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3MouseiggV2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr7 | 158821295 | 158821493 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3NakeddnaV2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr18 | 76116971 | 76117171 | 76117153 |
| chr21 | 46944298 | 46944346 | 46944323 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3ifngStat1V2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374635 | 135374801 | 135374737 |
| chr21 | 46944272 | 46944358 | 46944323 |
| chr7 | 158821403 | 158821504 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHepg2Pol2V2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374659 | 135374859 | 135374737 |
| chr21 | 46944180 | 46944350 | 46944323 |
| chr7 | 158821338 | 158821458 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHepg2Srebp2V2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr15 | 100338749 | 100338949 | 100338915 |
| chr21 | 46944293 | 46944365 | 46944323 |
| chr7 | 158821363 | 158821465 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalRep1K562InputV2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374725 | 135374834 | 135374737 |
| chr18 | 76117110 | 76117170 | 76117153 |
| chr21 | 46944309 | 46944357 | 46944323 |
| chr8 | 146274642 | 146274842 | 146274826 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3Ap2gamma y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr18 | 76117110 | 76117310 | 76117153 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3Tr4 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374719 | 135374830 | 135374737 |
| chr18 | 76117014 | 76117167 | 76117153 |
| chr21 | 46944290 | 46944373 | 46944323 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Bdp1 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374658 | 135374858 | 135374737 |
| chr7 | 158821339 | 158821512 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Brf1 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374636 | 135374836 | 135374737 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Rpc155 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374686 | 135374806 | 135374737 |
| chr18 | 76116997 | 76117197 | 76117153 |
| chr20 | 62435792 | 62435992 | 62435964 |
| chr21 | 46944315 | 46944364 | 46944323 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Sirt6 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr15 | 100338808 | 100338936 | 100338915 |
| chr21 | 46944311 | 46944343 | 46944323 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562bGata2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374699 | 135374798 | 135374737 |
| chr18 | 76117107 | 76117278 | 76117153 |
| chr21 | 46944184 | 46944384 | 46944323 |
| chr7 | 158821407 | 158821445 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562bTr4 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374727 | 135374855 | 135374737 |
| chr15 | 100338814 | 100338925 | 100338915 |
| chr8 | 146274629 | 146274829 | 146274826 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562bYy1 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374719 | 135374848 | 135374737 |
| chr18 | 76117069 | 76117159 | 76117153 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalNt2d1Suz12 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374657 | 135374857 | 135374737 |
| chr7 | 158821351 | 158821502 | 158821424 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalNt2d1Yy1 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr7 | 158821340 | 158821487 | 158821424 |
delete from wgEncodeYaleChIPseqRel2SignalGm12878Input where chrom = "chr18" and chromEnd = 76117288;
delete from wgEncodeYaleChIPseqRel2SignalHct116Input where chrom = "chr10" and chromEnd = 135374848;
delete from wgEncodeYaleChIPseqRel2SignalHct116Input where chrom = "chr15" and chromEnd = 100338933;
delete from wgEncodeYaleChIPseqRel2SignalHek293Input where chrom = "chr21" and chromEnd = 46944346;
delete from wgEncodeYaleChIPseqRel2SignalHek293Input where chrom = "chr7" and chromEnd = 158821462;
delete from wgEncodeYaleChIPseqRel2SignalHelas3ifngInput where chrom = "chr21" and chromEnd = 46944345;
delete from wgEncodeYaleChIPseqRel2SignalHepg2Input where chrom = "chr15" and chromEnd > 100338915;
delete from wgEncodeYaleChIPseqSignalHelas3LargefragmentV2 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalHelas3LargefragmentV2 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalHelas3LargefragmentV2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalHelas3MnaseV2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalHelas3MouseiggV2 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalHelas3NakeddnaV2 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalHelas3NakeddnaV2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalHelas3ifngStat1V2 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalHelas3ifngStat1V2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalHelas3ifngStat1V2 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalHepg2Pol2V2 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalHepg2Pol2V2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalHepg2Pol2V2 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalHepg2Srebp2V2 where chrom = "chr15" and chromEnd > 100338915;
delete from wgEncodeYaleChIPseqSignalHepg2Srebp2V2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalHepg2Srebp2V2 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalRep1K562InputV2 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalRep1K562InputV2 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalRep1K562InputV2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalRep1K562InputV2 where chrom = "chr8" and chromEnd > 146274826;
delete from wgEncodeYaleChIPseqSignalHelas3Ap2gamma where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalHelas3Tr4 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalHelas3Tr4 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalHelas3Tr4 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalK562Bdp1 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalK562Bdp1 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalK562Brf1 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalK562Rpc155 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalK562Rpc155 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalK562Rpc155 where chrom = "chr20" and chromEnd > 62435964;
delete from wgEncodeYaleChIPseqSignalK562Rpc155 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalK562Sirt6 where chrom = "chr15" and chromEnd > 100338915;
delete from wgEncodeYaleChIPseqSignalK562Sirt6 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalK562bGata2 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalK562bGata2 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalK562bGata2 where chrom = "chr21" and chromEnd > 46944323;
delete from wgEncodeYaleChIPseqSignalK562bGata2 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalK562bTr4 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalK562bTr4 where chrom = "chr15" and chromEnd > 100338915;
delete from wgEncodeYaleChIPseqSignalK562bTr4 where chrom = "chr8" and chromEnd > 146274826;
delete from wgEncodeYaleChIPseqSignalK562bYy1 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalK562bYy1 where chrom = "chr18" and chromEnd > 76117153;
delete from wgEncodeYaleChIPseqSignalNt2d1Suz12 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalNt2d1Suz12 where chrom = "chr7" and chromEnd > 158821424;
delete from wgEncodeYaleChIPseqSignalNt2d1Yy1 where chrom = "chr7" and chromEnd > 158821424;
# Note: should have updated those rows to end at chrom size. Oh well, that is not a big problem as we are talking extreme telemere here.
# additional ones:
hg18.wgEncodeYaleChIPseqRel2SignalHelas3Input has 2 records with end > chromSize.
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqRel2SignalHelas3Input y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr18 | 76117124 | 76117324 | 76117153 |
| chr21 | 46944169 | 46944343 | 46944323 |
update wgEncodeYaleChIPseqRel2SignalHelas3Input set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153;
update wgEncodeYaleChIPseqRel2SignalHelas3Input set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323;
hg18.wgEncodeYaleChIPseqSignalGm12878NfkbTnfa has 4 records with end > chromSize.
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalGm12878NfkbTnfa y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374723 | 135374857 | 135374737 |
| chr15 | 100338748 | 100338948 | 100338915 |
| chr18 | 76117093 | 76117291 | 76117153 |
| chr20 | 62435767 | 62435967 | 62435964 |
update wgEncodeYaleChIPseqSignalGm12878NfkbTnfa set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalGm12878NfkbTnfa set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqSignalGm12878NfkbTnfa set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153;
update wgEncodeYaleChIPseqSignalGm12878NfkbTnfa set chromEnd = 62435964 where chrom = "chr20" and chromEnd > 62435964;
hg18.wgEncodeYaleChIPseqSignalHelas3E2f4 has 4 records with end > chromSize.
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3E2f4 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374630 | 135374830 | 135374737 |
| chr18 | 76117005 | 76117160 | 76117153 |
| chr21 | 46944197 | 46944335 | 46944323 |
| chr7 | 158821414 | 158821471 | 158821424 |
update wgEncodeYaleChIPseqSignalHelas3E2f4 set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalHelas3E2f4 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalHelas3E2f4 set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153;
update wgEncodeYaleChIPseqSignalHelas3E2f4 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323;
hg18.wgEncodeYaleChIPseqSignalHelas3Ha has 3 records with end > chromSize.
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3Ha y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374662 | 135374833 | 135374737 |
| chr18 | 76117082 | 76117282 | 76117153 |
| chr7 | 158821417 | 158821447 | 158821424 |
update wgEncodeYaleChIPseqSignalHelas3Ha set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalHelas3Ha set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalHelas3Ha set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153;
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Nfyb y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr7 | 158821281 | 158821466 | 158821424 |
update wgEncodeYaleChIPseqSignalK562Nfyb set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
2009-10-13 Past due update status
=================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 279 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 315 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 316 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 317 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 318 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 319 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 320 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 323 approved
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2009-10-14 Release 2 out the door !!!
=====================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 released
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# Seth Frietz feedback:
# > I want to inform you about one correction needed for a specific dataset.
# > The dataset ‘HA’ should actually say HA E2F1. This data was generated
# > with an HA tagged version of E2F1. This is important because down the
# > road we and others will be using HA tagged versions of several different proteins.
### Oh well. I thought it was perfect for a moment.
2009-10-21 More submissions
===========================
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/739/out/fileDb.ra | grep parentTable > tmp.txt
/cluster/data/encode/pipeline/bin/encodeStatus.pl 739 displayed
hg18.wgEncodeYaleChIPseqSignalHelas3E2f6 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Nfyb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878NfkbTnfa has 1 records with end > chromSize.
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalHelas3E2f6 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374721 | 135374829 | 135374737 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Nfyb y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
Empty set (7.85 sec)
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalGm12878NfkbTnfa y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
Empty set (5 min 50.55 sec)
update wgEncodeYaleChIPseqSignalHelas3E2f6 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
Query OK, 1 row affected (3 min 1.25 sec)
### Look for more problems with K562b renaming
K562b/E2f4
K562b/E2f6
K562b/GATA-1 * Fine
K562b/GATA-2
K562b/SETDB1
K562b/TR4
K562b/YY1
K562b/ZNF263 * fixed
HepG2b/TR4
2009-11-24 Finally the corrected tagAligns
==========================================
Several problems were fixed by hand editing DAF/DDFs
1) Mike Wilson submitted DDFs with multiple lines per dataset!
2) The DAF matchFirst had to change from 32 to 30.
3) Several types such as Jun instead of c-Jun
4) He include PolyA RNA which is a no no.
To solve this I create an rna subdir for 634, then move the data files and create a daf/ddf.
Then
tar -cpzf YDH_RnaSeq_tagAlign_update.tgz *
submitted as 788
Notice that 276 is marked as released but it is only displayed
update projects set status = 'displayed' where id = 276;
# submission id's that must be finished up:
select id,name,status,user_id from projects where name like "Y%" and status != "released";
+-----+-------------------------+-----------+---------+
| id | name | status | user_id |
+-----+-------------------------+-----------+---------+
| 276 | YHD_K562_PolyA_RNA | displayed | 6 |
| 539 | YDH_GM12878_ds_cDNA | displayed | 6 |
| 540 | YDH_K562_IFNa30m_cDNA | displayed | 6 |
| 541 | YDH_K562_IFNa6h_cDNA | displayed | 6 |
| 542 | YDH_K562_IFNg30m_cDNA | displayed | 6 |
| 543 | YDH_K562_IFNg6h_cDNA | displayed | 6 |
| 633 | YDH_tagAlign_update_v3 | loaded | 6 |
| 634 | YDH_tagAlign_update | loaded | 6 |
| 669 | YDH_K562_Pol3 | loaded | 6 |
| 739 | YDH_HeLa-S3_E2F6 | displayed | 6 |
| 757 | YDH_MCF-7_HA-E2F1 | loaded | 6 |
| 787 | YDH_tagAlign_update2 | loaded | 6 |
| 788 | YDH_tagAlign_update_RNA | loaded | 6 |
+-----+-------------------------+-----------+---------+
13 rows in set (0.01 sec)
cd {downloadsDir}
cp fileDb.ra fileDb.ra.2009-12-01
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/633/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/634/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/669/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/757/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/787/out/fileDb.ra | grep parentTable >> tmp.txt
e tmp.txt
# remove old from dir after confirming all are linked to release1/ or release2/:
rm wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cfos.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cfos.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Gm12878Cfos.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Gm12878Jund.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm12878Jund.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Gm12878Max.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm12878Max.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol3.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol3.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hct116Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hct116Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hct116Tcf4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hct116Tcf4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hek293Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hek293Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Hek293Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Cfos.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Cfos.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Cmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Cmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Largefragment.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Largefragment.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Max.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Max.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Mnase.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Mnase.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Helas3Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hepg2Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hepg2Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Hepg2Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hepg2Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hepg2Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Hepg2Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hepg2Srebp1a.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hepg2Srebp1a.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Hepg2Srebp1a.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hepg2Srebp2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hepg2Srebp2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Hepg2Srebp2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Hepg2bTr4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Hepg2bTr4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Bdp1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Bdp1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3K562Bdp1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Brf1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Brf1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep3K562Brf1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Cjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Cjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562InputV2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562InputV2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Jund.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Jund.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Max.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Max.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Nfe2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Nfe2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Rad21.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Rad21.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Rpc155.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Rpc155.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Sirt6.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Sirt6.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Xrcc4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Xrcc4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bE2f4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bE2f4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bE2f6.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bE2f6.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bGata2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bGata2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bTr4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bTr4.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bYy1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bYy1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562bZnf263.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bZnf263.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Nt2d1Suz12.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Nt2d1Suz12.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Nt2d1Yy1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Nt2d1Yy1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsHct116Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsHek293Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsHepg2bInput.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsNt2d1Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3ifngStat1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3ifngStat1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hCjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hCjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifng30Cjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifng30Cjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hCjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hCjun.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Cmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Cmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hCmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hCmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hCmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hCmyc.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsK562Ifna30Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsK562Ifna6hInput.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsK562Ifng30Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsK562Ifng6hInput.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hPol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hPol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hPol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hPol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Stat1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Stat1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hStat1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hStat1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Stat2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Stat2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hStat2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hStat2.tagAlign.gz
grep -v wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cfos\.tagAlign\.gz fileDb.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cfos\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep3Gm12878Cfos\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Gm12878Jund\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2Gm12878Jund\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1Gm12878Max\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Gm12878Max\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol3\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol3\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hct116Pol2\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2Hct116Pol2\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hct116Tcf4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Hct116Tcf4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hek293Pol2\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2Hek293Pol2\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep3Hek293Pol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Cfos\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Cfos\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Cmyc\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Cmyc\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Largefragment\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Largefragment\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Max\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Max\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Mnase\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Mnase\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Mouseigg\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Mouseigg\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3Pol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3Pol2\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep3Helas3Pol2\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hepg2Input\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Hepg2Input\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep3Hepg2Input\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1Hepg2Pol2\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2Hepg2Pol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep3Hepg2Pol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hepg2Srebp1a\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2Hepg2Srebp1a\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep3Hepg2Srebp1a\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hepg2Srebp2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Hepg2Srebp2\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep3Hepg2Srebp2\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1Hepg2bTr4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Hepg2bTr4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Bdp1\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Bdp1\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep3K562Bdp1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Brf1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Brf1\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep3K562Brf1\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Cjun\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Cjun\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562InputV2\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562InputV2\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Jund\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Jund\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Max\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Max\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Nfe2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Nfe2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Pol2\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Pol2\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Rad21\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Rad21\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Rpc155\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Rpc155\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Sirt6\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Sirt6\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Xrcc4\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Xrcc4\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bE2f4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bE2f4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bE2f6\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bE2f6\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bGata2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bGata2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bTr4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bTr4\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bYy1\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bYy1\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562bZnf263\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562bZnf263\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1Nt2d1Suz12\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep2Nt2d1Suz12\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep1Nt2d1Yy1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2Nt2d1Yy1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsGm12878Input\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsHct116Input\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsHek293Input\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsHepg2bInput\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsNt2d1Input\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1Helas3ifngStat1\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2Helas3ifngStat1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hCjun\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hCjun\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifng30Cjun\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifng30Cjun\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hCjun\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hCjun\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Cmyc\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Cmyc\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hCmyc\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hCmyc\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hCmyc\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hCmyc\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsK562Ifna30Input\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsK562Ifna6hInput\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsK562Ifng30Input\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsK562Ifng6hInput\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Pol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Pol2\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hPol2\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hPol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hPol2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hPol2\.tagAlign\.gz > tmpB.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Stat1\.tagAlign\.gz tmpB.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Stat1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hStat1\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hStat1\.tagAlign\.gz > tmpA.ra
grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Stat2\.tagAlign\.gz tmpA.ra | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Stat2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hStat2\.tagAlign\.gz | grep -v wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hStat2\.tagAlign\.gz > tmpB.ra
# edit tmp.txt to get all the proper metadata (big job)
wl tmpB.ra 276 tmpB.ra
wl tmpA.ra 280 tmpA.ra
wl fileDb.ra 407 fileDb.ra
cat tmp.txt >> tmpB.ra
mv tmpB.ra fileDb.ra
wl fileDb.ra 414 fileDb.ra
# edit preamble.html and
encodeDownloadsPage.pl index.html
# awkward name changes (all others are simple V2 (or V3) suffixes):
wgEncodeYaleChIPseqAlignmentsRep1Gm12878Inputv2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1Hct116Inputv2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsHct116Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1Hek293Inputv2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsHek293Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1Hepg2bInputv2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsHepg2bInput.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1Nt2d1Inputv2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsNt2d1Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2Nt2d1Inputv2.tagAlign.gz < ???
wgEncodeYaleChIPseqAlignmentsRep1K562InputIfna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsK562Ifna30Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562InputIfna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsK562Ifna6hInput.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562InputIfng30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsK562Ifng30Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562InputIfng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsK562Ifng6hInput.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1Helas3Stat1IfngV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1Helas3ifngStat1.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2Helas3Stat1IfngV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2Helas3ifngStat1.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562CjunIfna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hCjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562CjunIfna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hCjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562CjunIfng30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifng30Cjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562CjunIfng30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifng30Cjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562CjunIfng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hCjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562CjunIfng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hCjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562CmycIfna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Cmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562CmycIfna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Cmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562CmycIfna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hCmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562CmycIfna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hCmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562CmycIfng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hCmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562CmycIfng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hCmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Pol2Ifna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Pol2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Pol2Ifna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Pol2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Pol2Ifna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hPol2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Pol2Ifna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hPol2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Pol2Ifng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifng6hPol2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Pol2Ifng6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifng6hPol2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Stat1Ifna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Stat1.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Stat1Ifna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Stat1.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Stat1Ifna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hStat1.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Stat1Ifna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hStat1.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Stat2Ifna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna30Stat2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Stat2Ifna30V2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna30Stat2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Stat2Ifna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep1K562Ifna6hStat2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562Stat2Ifna6hV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsRep2K562Ifna6hStat2.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1Helas3LargefragmentV2.tagAlign.gz < wgEncodeYaleChIPseqRel2AlignmentsRep1Helas3Largefragment.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2Helas3LargefragmentV2.tagAlign.gz < wgEncodeYaleChIPseqRel2AlignmentsRep2Helas3Largefragment.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562InputV3.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsK562Input.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2K562InputV3.tagAlign.gz < ???
wgEncodeYaleChIPseqAlignmentsRep1K562bInputV2.tagAlign.gz < wgEncodeYaleChIPseqAlignmentsK562bInput.tagAlign.gz
# These tagAligns were not corrected:
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=K562 antibody=c-Fos fragLength=200 view=Alignments replicate=1 dataVersion="ENCODE Nov 2008 Freeze" subId=68 dateSubmitted=2008-11-21 dateUnrestricted=2009-08-21 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep1K562Cfos fileName=wgEncodeYaleChIPseqAlignmentsRep1K562Cfos.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=K562 antibody=c-Fos fragLength=200 view=Alignments replicate=2 dataVersion="ENCODE Nov 2008 Freeze" subId=68 dateSubmitted=2008-11-21 dateUnrestricted=2009-08-21 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep2K562Cfos fileName=wgEncodeYaleChIPseqAlignmentsRep2K562Cfos.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=K562 antibody=c-Fos fragLength=200 view=Alignments replicate=3 dataVersion="ENCODE Nov 2008 Freeze" subId=68 dateSubmitted=2008-11-21 dateUnrestricted=2009-08-21 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep3K562Cfos fileName=wgEncodeYaleChIPseqAlignmentsRep3K562Cfos.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=K562 antibody=c-Myc fragLength=200 view=Alignments replicate=1 dataVersion="ENCODE Nov 2008 Freeze" subId=69 dateSubmitted=2008-11-21 dateUnrestricted=2009-08-21 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep1K562Cmyc fileName=wgEncodeYaleChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=K562 antibody=c-Myc fragLength=200 view=Alignments replicate=2 dataVersion="ENCODE Nov 2008 Freeze" subId=69 dateSubmitted=2008-11-21 dateUnrestricted=2009-08-21 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep2K562Cmyc fileName=wgEncodeYaleChIPseqAlignmentsRep2K562Cmyc.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=UCD(Farnham) dataType=ChIPseq cell=K562b antibody=GATA-1 fragLength=200 view=Alignments replicate=1 labVersion="Fragmented using Bioruptor, precipitated with protein A agarose beads, PeakSeq 1.0 (fdr 0.001)" dataVersion="ENCODE Feb 2009 Freeze" subId=227 dateSubmitted=2009-02-27 dateUnrestricted=2009-11-27 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep1K562bGata1 fileName=wgEncodeYaleChIPseqAlignmentsRep1K562bGata1.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=UCD(Farnham) dataType=ChIPseq cell=K562b antibody=GATA-1 fragLength=200 view=Alignments replicate=2 labVersion="Fragmented using Bioruptor, precipitated with protein A agarose beads, PeakSeq 1.0 (fdr 0.001)" dataVersion="ENCODE Feb 2009 Freeze" subId=227 dateSubmitted=2009-02-27 dateUnrestricted=2009-11-27 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep2K562bGata1 fileName=wgEncodeYaleChIPseqAlignmentsRep2K562bGata1.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=NB4 antibody=Input fragLength=200 view=Alignments dataVersion="ENCODE Nov 2008 Freeze" subId=107 dateSubmitted=2009-02-25 dateUnrestricted=2009-11-25 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalNb4Input fileName=wgEncodeYaleChIPseqAlignmentsNb4Input.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=NB4 antibody=Input fragLength=200 view=Alignments dataVersion="ENCODE Nov 2008 Freeze" subId=19 dateSubmitted=2008-10-31 dateUnrestricted=2009-07-31 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalNb4Input fileName=wgEncodeYaleChIPseqAlignmentsNb4Input.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=NB4 antibody=Pol2 fragLength=200 view=Alignments replicate=1 dataVersion="ENCODE Feb 2009 Freeze" subId=18 dateSubmitted=2008-10-31 dateUnrestricted=2009-07-31 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep1Nb4Pol2 fileName=wgEncodeYaleChIPseqAlignmentsRep1Nb4Pol2.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=NB4 antibody=Pol2 fragLength=200 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=18 dateSubmitted=2008-10-31 dateUnrestricted=2009-07-31 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep2Nb4Pol2 fileName=wgEncodeYaleChIPseqAlignmentsRep2Nb4Pol2.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=ChIPseq cell=NB4 antibody=Pol2 fragLength=200 view=Alignments replicate=3 dataVersion="ENCODE Feb 2009 Freeze" subId=18 dateSubmitted=2008-10-31 dateUnrestricted=2009-07-31 composite=wgEncodeYaleChIPseq parentTable=wgEncodeYaleChIPseqRawSignalRep3Nb4Pol2 fileName=wgEncodeYaleChIPseqAlignmentsRep3Nb4Pol2.tagAlign.gz
metadata project=wgEncode grant=Snyder lab=Yale(Snyder) dataType=RnaSeqPolya cell=K562 fragLength=200 view=Alignments dataVersion="ENCODE Feb 2009 Freeze" subId=276 dateSubmitted=2009-03-17 dateUnrestricted=2009-12-17 composite=wgEncodeYaleRnaSeqPolya parentTable=wgEncodeYaleRnaSeqPolyaRawSignalK562 fileName=wgEncodeYaleRnaSeqPolyaAlignmentsK562.tagAlign.gz
/cluster/data/encode/pipeline/bin/encodeStatus.pl 633 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 634 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 669 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 757 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 787 displayed
## Now RnaPolyA
cd ../wgEncodeYaleRNAseq/
mv ../wgEncodeYaleRnaSeqPolya/wgEncodeYaleRnaSeqPolyaAlignmentsK562V2.tagAlign.gz .cp fileDb.ra fileDb.ra.2009-12-01
# Bad dir!
rm -rf ../wgEncodeYaleRnaSeqPolya
cp fileDb.ra fileDb.ra.2009-12-01
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/788/out/fileDb.ra | grep parentTable > tmp.txt
e tmp.txt
# actually one line is just moved to fileDb.ra and old version removed.
# Since no public release yet, then this will be renamed as a replacement, not V2
mkdir old
mv wgEncodeYaleRnaSeqPolyaAlignmentsK562.tagAlign.gz old
mv wgEncodeYaleRnaSeqPolyaAlignmentsK562V2.tagAlign.gz wgEncodeYaleRnaSeqPolyaAlignmentsK562.tagAlign.gz
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 788 displayed
### Some chrom overruns:
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalK562Pol3 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374660 | 135374860 | 135374737 |
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeYaleChIPseqSignalMcf7Hae2f1 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chr10 | 135374719 | 135374805 | 135374737 |
delete from wgEncodeYaleChIPseqSignalK562Pol3 where chrom = "chr10" and chromEnd > 135374737;
delete from wgEncodeYaleChIPseqSignalMcf7Hae2f1 where chrom = "chr10" and chromEnd > 135374737;
### Some more name mismatch overrides:
cd {downloadsDir}
rm wgEncodeYaleChIPseqRel2AlignmentsRep1Helas3Largefragment.tagAlign.gz
rm wgEncodeYaleChIPseqRel2AlignmentsRep2Helas3Largefragment.tagAlign.gz
grep -v wgEncodeYaleChIPseqRel2AlignmentsRep1Helas3Largefragment\.tagAlign\.gz fileDb.ra | grep -v wgEncodeYaleChIPseqRel2AlignmentsRep2Helas3Largefragment\.tagAlign\.gz > tmpA.txt
wl tmpA.txt 412 tmpA.txt
wl fileDb.ra 414 fileDb.ra
mv tmpA.txt fileDb.ra
rm wgEncodeYaleChIPseqAlignmentsK562Input.tagAlign.gz
grep -v wgEncodeYaleChIPseqAlignmentsK562Input\.tagAlign\.gz fileDb.ra > tmpA.txt
wl tmpA.txt 410 tmpA.txt
wl fileDb.ra 412 fileDb.ra
mv tmpA.txt fileDb.ra
rm wgEncodeYaleChIPseqAlignmentsK562bInput.tagAlign.gz
wl tmpA.txt 409 tmpA.txt
wl fileDb.ra 410 fileDb.ra
mv tmpA.txt fileDb.ra
### Okay, this is what I believe to be the complete list of uncorrected tagAligns
wgEncodeYaleChIPseqAlignmentsHelas3ifngInput.tagAlign.gz 477M 2008-10-31 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsHelas3Input.tagAlign.gz 571M 2008-10-31 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep1Helas3Nakeddna.tagAlign.gz 291M 2009-02-25 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsRep2Helas3Nakeddna.tagAlign.gz 231M 2009-02-25 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsRep3Helas3Nakeddna.tagAlign.gz 221M 2009-02-25 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsRep1K562Cfos.tagAlign.gz 115M 2008-11-21 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep2K562Cfos.tagAlign.gz 95M 2008-11-21 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep3K562Cfos.tagAlign.gz 123M 2008-11-21 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz 115M 2008-11-21 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep2K562Cmyc.tagAlign.gz 120M 2008-11-21 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep1K562bGata1.tagAlign.gz 120M 2009-02-27 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsRep2K562bGata1.tagAlign.gz 235M 2009-02-27 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsNb4Input.tagAlign.gz 195M 2009-02-25 ENCODE Nov 2008 Freeze
wgEncodeYaleChIPseqAlignmentsRep1Nb4Pol2.tagAlign.gz 192M 2008-10-31 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsRep2Nb4Pol2.tagAlign.gz 117M 2008-10-31 ENCODE Feb 2009 Freeze
wgEncodeYaleChIPseqAlignmentsRep3Nb4Pol2.tagAlign.gz 93M 2008-10-31 ENCODE Feb 2009 Freeze
# edit fileDb.ra to mark all in the above list as "uncorrected". Edit preamble.html to make this explicit.
encodeDownloadsPage.pl index.html
2010-01-05 Begin Jan 15th freeze
================================
Test of Jim's encodePatchTdb
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/853/out/trackDb.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/853/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/860/out/trackDb.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/860/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/trackDb.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/862/out/trackDb.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/863/out/trackDb.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/864/out/trackDb.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/888/out/trackDb.ra
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/889/out/trackDb.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/862/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/863/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/864/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/888/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/889/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
### Problem with 889!!! It conflicts with dataset
Submitted 2009-02-25: wgEncodeYaleChIPseqPeaksHelas3Mouseigg
Versioned 2009-07-21: wgEncodeYaleChIPseqSignalHelas3MouseiggV2
Incoming 2010-01-06: wgEncodeYaleChIPseqSignalHelas3Mouseigg
### TODO: Awaiting response from Mike Wilson
# Resolution: the newer one is a duplicate of the old so unload and delete 889
# changed long label
encodePatchTdb -mode=replace -noComment /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb -mode=replace -noComment /hive/groups/encode/dcc/pipeline/encpipeline_prod/862/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb -mode=replace -noComment /hive/groups/encode/dcc/pipeline/encpipeline_prod/863/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb -mode=replace -noComment /hive/groups/encode/dcc/pipeline/encpipeline_prod/864/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
encodePatchTdb -mode=replace -noComment /hive/groups/encode/dcc/pipeline/encpipeline_prod/888/out/trackDb.ra ~/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
cd {downloadsDir}
cp fileDb.ra fileDb.ra.2010-10-06
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/853/out/fileDb.ra | grep parentTable > tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/860/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/862/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/863/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/864/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/888/out/fileDb.ra | grep parentTable >> tmp.txt
e tmp.txt
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html
# done with 7 of 8.
/cluster/data/encode/pipeline/bin/encodeStatus.pl 853 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 860 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 861 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 862 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 863 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 864 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 888 displayed
2010-01-12 All IgGs must be reloaded with a protocol
====================================================
| 861 | YDH_GM10847_IgG_Control | displayed | 6 |
| 862 | YDH_GM10847_IgG_Pol2 | displayed | 6 |
| 863 | YDH_GM12891_IgG_Control | displayed | 6 |
| 864 | YDH_K562_IgG_Control | displayed | 6 |
| 865 | YDH_GM12891_IgG_Pol2 | validate requested | 6 |
| 888 | YDH_HeLa-S3_IgG_BAF155 | displayed | 6 |
| 890 | YDH_HeLa-S3_IgG_BAF170 | validate requested | 6 |
| 891 | YDH_HeLa-S3_IgG_Brg1 | validate requested | 6 |
| 892 | YDH_HeLa-S3_IgG_Ini1 | validate requested | 6 |
| 893 | YDH_K562_IgG_Brg1 | validating | 6 |
| 894 | YDH_K562_IgG_Ini1 | validating | 6 |
| 895 | YDH_K562_IgG_Pol2 | validating | 6 |
| 941 | YDH_GM12892_IgG_NFKB | validate requested | 6 |
| 942 | YDH_GM18526_IgG_NFKB | validate requested | 6 |
| 943 | YDH_GM12878_IgG_NFKB | validate requested | 6 |
| 945 | YDH_GM18505_IgG_NFKB | validate requested | 6 |
| 946 | YDH_GM19099_IgG_NFKB | validate requested | 6 |
| 947 | YDH_GM19193_IgG_NFKB | validate requested | 6 |
| 956 | YDH_GM12878_IgG_Control | validate requested | 6 |
| 957 | YDH_GM12878_IgG_Pol2 | loaded | 6 |
| 959 | YDH_GM12892_IgG_Control | validate requested | 6 |
| 996 | YDH_GM15510_IgG_Control | validate requested | 6 |
| 997 | YDH_GM15510_IgG_Pol2 | validate requested | 6 |
| 999 | YDH_HeLa-S3_IgG_Nrf1 | validate failed | 6 |
1008
1016
1020
1024
1025
1029
# TODO
1) unload/reload all IgGs (done)
2) Remove any no longer appropriate download only files or tables
3) Bring K562/Pol2, GM12878/Pol2 or any other stepped on tables/files back to life.
# After the freeze:
select id,name,status,user_id from projects where status = "loaded" and user_id = 6 order by id;
+------+--------------------------------+--------+---------+
| id | name | status | user_id |
+------+--------------------------------+--------+---------+
| 861 | YDH_GM10847_IgG_Control | loaded | 6 |
| 862 | YDH_GM10847_IgG_Pol2 | loaded | 6 |
| 863 | YDH_GM12891_IgG_Control | loaded | 6 |
| 864 | YDH_K562_IgG_Control | loaded | 6 |
| 865 | YDH_GM12891_IgG_Pol2 | loaded | 6 |
| 888 | YDH_HeLa-S3_IgG_BAF155 | loaded | 6 |
| 890 | YDH_HeLa-S3_IgG_BAF170 | loaded | 6 |
| 891 | YDH_HeLa-S3_IgG_Brg1 | loaded | 6 |
| 892 | YDH_HeLa-S3_IgG_Ini1 | loaded | 6 |
| 893 | YDH_K562_IgG_Brg1 | loaded | 6 |
| 894 | YDH_K562_IgG_Ini1 | loaded | 6 |
| 895 | YDH_K562_IgG_Pol2 | loaded | 6 |
| 900 | YDH_GM12878_TR4 | loaded | 6 |
| 928 | YDH_HeLa-S3_E2F1 | loaded | 6 |
| 933 | YDH_GM12878_ZZZ3 | loaded | 6 |
| 941 | YDH_GM12892_IgG_NFKB | loaded | 6 |
| 942 | YDH_GM18526_IgG_NFKB | loaded | 6 |
| 943 | YDH_GM12878_IgG_NFKB | loaded | 6 |
| 945 | YDH_GM18505_IgG_NFKB | loaded | 6 |
| 946 | YDH_GM19099_IgG_NFKB | loaded | 6 |
| 947 | YDH_GM19193_IgG_NFKB | loaded | 6 |
| 950 | YDH_HUVEC_Pol2 | loaded | 6 |
| 951 | YDH_K562_ATF3 | loaded | 6 |
| 952 | YDH_K562_NELFe | loaded | 6 |
| 956 | YDH_GM12878_IgG_Control | loaded | 6 |
| 957 | YDH_GM12878_IgG_Pol2 | loaded | 6 |
| 959 | YDH_GM12892_IgG_Control | loaded | 6 |
| 974 | YDH_K562_IFNg30_Pol2 | loaded | 6 |
| 975 | YDH_K562_GTF2B | loaded | 6 |
| 995 | YDH_HUVEC_Jun | loaded | 6 |
| 996 | YDH_GM15510_IgG_Control | loaded | 6 |
| 997 | YDH_GM15510_IgG_Pol2 | loaded | 6 |
| 999 | YDH_HeLa-S3_IgG_Nrf1 | loaded | 6 |
| 1008 | YDH_GM12892_IgG_Pol2 | loaded | 6 |
| 1016 | YDH_GM18505_IgG_Pol2 | loaded | 6 |
| 1020 | YHD_GM18505_IgG_Control | loaded | 6 |
| 1024 | YDH_GM18526_IgG_Pol2 | loaded | 6 |
| 1025 | YDH_GM18526_IgG_Control | loaded | 6 |
| 1029 | YDH_GM18951_IgG_Pol2 | loaded | 6 |
| 1030 | YDH_HeLa-S3_IgG_Rabbit_Control | loaded | 6 |
| 1031 | YDH_HeLa-S3_IgG_Rabbit_c-Jun | loaded | 6 |
| 1032 | YDH_HeLa-S3_IgG_Rabbit_JunD | loaded | 6 |
| 1044 | YDH_GM18951_IgG_Control | loaded | 6 |
| 1045 | YDH_GM19099_IgG_Control | loaded | 6 |
| 1046 | YDH_GM19099_IgG_Pol2 | loaded | 6 |
| 1047 | YDH_GM19193_IgG_Control | loaded | 6 |
| 1048 | YDH_GM19193_IgG_Pol2 | loaded | 6 |
| 1050 | YDH_GM10847_IgG_NFKB | loaded | 6 |
| 1051 | YDH_GM12891_IgG_NFKB | loaded | 6 |
| 1052 | YDH_GM15510_IgG_NFKB | loaded | 6 |
| 1053 | YDH_GM18951_IgG_NFKB | loaded | 6 |
| 1058 | YDH_K562_IFNg30_STAT1 | loaded | 6 |
| 1059 | YDH_K562_IFNg6h_STAT1 | loaded | 6 |
| 1062 | YDH_HepG2_Forskolin_CEBPB | loaded | 6 |
| 1063 | YHD_HepG2_Forskolin_ERRA | loaded | 6 |
| 1066 | YHD_HepG2_Forskolin_Control | loaded | 6 |
| 1067 | YHD_HepG2_Forskolin_GRp20 | loaded | 6 |
| 1068 | YHD_HepG2_Forskolin_HNF4A | loaded | 6 |
| 1069 | YHD_HepG2_Forskolin_HSF1 | loaded | 6 |
| 1070 | YHD_HepG2_Insulin_Control | loaded | 6 |
| 1071 | YHD_HepG2_Forskolin_PGC1A | loaded | 6 |
| 1072 | YHD_HepG2_Forskolin_Pol2 | loaded | 6 |
| 1073 | YHD_HepG2_Insulin_SREBP1 | loaded | 6 |
| 1076 | YDH_GM12878_Rad21 | loaded | 6 |
| 1077 | YDH_HeLa-S3_TFIIIC | loaded | 6 |
| 1078 | YDH_HeLa-S3_Bdp1 | loaded | 6 |
| 1081 | YDH_K562_TFIIIC | loaded | 6 |
| 1082 | YDH_HeLa-S3_RPC155 | loaded | 6 |
| 1083 | YDH_K562_Brf2 | loaded | 6 |
| 1085 | YDH_HUVEC_Max | loaded | 6 |
| 1086 | YDH_HeLa-S3_Brf1 | loaded | 6 |
| 1087 | YDH_HeLa-S3_Brf2 | loaded | 6 |
| 1088 | YDH_K562b_MNase_SetDB1 | loaded | 6 |
+------+--------------------------------+--------+---------+
73 rows in set (0.00 sec)
Farnham GM12878 TR4 Loaded | 900 | YDH_GM12878_TR4 | loaded |
Farnham GM12878 YY1 Loaded
Farnham HeLa S3 E2F1 Loaded | 928 | YDH_HeLa-S3_E2F1 | loaded |
Farnham HeLa S3 E2F6 Displayed
Farnham K562b SetDB1 Loaded | 1088 | YDH_K562b_MNase_SetDB1 | loaded |
Farnham K562b ZNF274 Displayed
Farnham MCF-7 HA-E2F1 Displayed
Struhl GM12878 ZZZ3 Loaded | 933 | YDH_GM12878_ZZZ3 | loaded |
Struhl HeLa S3 Bdp1 Loaded | 1078 | YDH_HeLa-S3_Bdp1 | loaded |
Struhl HeLa S3 Brf1 Loaded | 1086 | YDH_HeLa-S3_Brf1 | loaded |
Struhl HeLa S3 Brf2 Loaded | 1087 | YDH_HeLa-S3_Brf2 | loaded |
Struhl HeLa S3 RPC155 Loaded | 1082 | YDH_HeLa-S3_RPC155 | loaded |
Struhl HeLa S3 TFIIIC Loaded | 1077 | YDH_HeLa-S3_TFIIIC | loaded |
Struhl K562 NELFe Loaded | 952 | YDH_K562_NELFe | loaded |
Synder GM10847/IgG Control Loaded | 861 | YDH_GM10847_IgG_Control | loaded |
Synder GM10847/IgG NFKB Loaded | 1050 | YDH_GM10847_IgG_NFKB | loaded |
Synder GM10847/IgG Pol II Loaded | 862 | YDH_GM10847_IgG_Pol2 | loaded |
Snyder GM12878 Rad21 Loaded | 1076 | YDH_GM12878_Rad21 | loaded |
Synder GM12878/IgG Control Loaded | 956 | YDH_GM12878_IgG_Control | loaded |
Synder GM12878/IgG NFKB Loaded | 943 | YDH_GM12878_IgG_NFKB | loaded |
Snyder GM12878/IgG Pol II Loaded | 957 | YDH_GM12878_IgG_Pol2 | loaded |
Synder GM12891/IgG Control Displayed | 863 | YDH_GM12891_IgG_Control | loaded |
Synder GM12891/IgG NFKB Loaded | 1051 | YDH_GM12891_IgG_NFKB | loaded |
Synder GM12891/IgG Pol II Loaded | 865 | YDH_GM12891_IgG_Pol2 | loaded |
Synder GM12892/IgG Control Loaded | 959 | YDH_GM12892_IgG_Control | loaded |
Synder GM12892/IgG NFKB Loaded | 941 | YDH_GM12892_IgG_NFKB | loaded |
Synder GM12892/IgG Pol II Loaded | 1008 | YDH_GM12892_IgG_Pol2 | loaded |
Synder GM15510/IgG Control Loaded | 996 | YDH_GM15510_IgG_Control | loaded |
Synder GM15510/IgG NFKB Loaded | 1052 | YDH_GM15510_IgG_NFKB | loaded |
Synder GM15510/IgG Pol II Loaded | 997 | YDH_GM15510_IgG_Pol2 | loaded |
Synder GM18505/IgG Control Loaded | 1020 | YHD_GM18505_IgG_Control | loaded |
Synder GM18505/IgG NFKB Loaded | 945 | YDH_GM18505_IgG_NFKB | loaded |
Synder GM18505/IgG Pol II Loaded | 1016 | YDH_GM18505_IgG_Pol2 | loaded |
Synder GM18526/IgG Control Loaded | 1025 | YDH_GM18526_IgG_Control | loaded |
Synder GM18526/IgG NFKB Loaded | 942 | YDH_GM18526_IgG_NFKB | loaded |
Synder GM18526/IgG Pol II Loaded | 1024 | YDH_GM18526_IgG_Pol2 | loaded |
Synder GM18951/IgG Control Loaded | 1044 | YDH_GM18951_IgG_Control | loaded |
Synder GM18951/IgG NFKB Loaded | 1053 | YDH_GM18951_IgG_NFKB | loaded |
Synder GM18951/IgG Pol II Loaded | 1029 | YDH_GM18951_IgG_Pol2 | loaded |
Synder GM19099/IgG Control Loaded | 1045 | YDH_GM19099_IgG_Control | loaded |
Synder GM19099/IgG NFKB Loaded | 946 | YDH_GM19099_IgG_NFKB | loaded |
Synder GM19099/IgG Pol II Loaded | 1046 | YDH_GM19099_IgG_Pol2 | loaded |
Synder GM19193/IgG Control Loaded | 1047 | YDH_GM19193_IgG_Control | loaded |
Synder GM19193/IgG NFKB Loaded | 947 | YDH_GM19193_IgG_NFKB | loaded |
Synder GM19193/IgG Pol II Loaded | 1048 | YDH_GM19193_IgG_Pol2 | loaded |
Snyder HeLa S3 IgG Loaded | 1030 | YDH_HeLa-S3_IgG_Rabbit_Control | loaded |
Snyder HeLa S3 Jun Loaded | 1031 | YDH_HeLa-S3_IgG_Rabbit_c-Jun | loaded |
Snyder HeLa S3 JunD Loaded | 1032 | YDH_HeLa-S3_IgG_Rabbit_JunD | loaded |
Snyder HeLa S3 Ini1 Loaded | 892 | YDH_HeLa-S3_IgG_Ini1 | loaded |
Snyder HeLa S3 NRF1 Loaded | 999 | YDH_HeLa-S3_IgG_Nrf1 | loaded |
Snyder HepG2/Insulin SREBP1 Loaded | 1073 | YHD_HepG2_Insulin_SREBP1 | loaded |
Snyder HepG2/Insulin Control Loaded | 1070 | YHD_HepG2_Insulin_Control | loaded |
Snyder HepG2/Forskolin HSF1 Loaded | 1069 | YHD_HepG2_Forskolin_HSF1 | loaded |
Snyder HepG2/Forskolin ERRA Loaded | 1063 | YHD_HepG2_Forskolin_ERRA | loaded |
Snyder HepG2/Forskolin HNF4A Loaded | 1068 | YHD_HepG2_Forskolin_HNF4A | loaded |
Snyder HepG2/Forskolin POL2 Loaded | 1072 | YHD_HepG2_Forskolin_Pol2 | loaded |
Snyder HepG2/Forskolin NRF2 Loaded
| 1071 | YHD_HepG2_Forskolin_PGC1A | loaded |
Snyder HepG2/Forskolin CEBPB Loaded | 1062 | YDH_HepG2_Forskolin_CEBPB | loaded |
Snyder HepG2/Forskolin GRp20 Loaded | 1067 | YHD_HepG2_Forskolin_GRp20 | loaded |
Snyder HepG2/Forskolin Control Loaded | 1066 | YHD_HepG2_Forskolin_Control | loaded |
Snyder HUVEC Jun Loaded | 995 | YDH_HUVEC_Jun | loaded |
Snyder HUVEC Max Loaded | 1085 | YDH_HUVEC_Max | loaded |
Snyder HUVEC Pol II Loaded | 950 | YDH_HUVEC_Pol2 | loaded |
Snyder K562/IFNg30' Pol II Loaded | 974 | YDH_K562_IFNg30_Pol2 | loaded |
Snyder K562/IFNg30' STAT1 Loaded | 1058 | YDH_K562_IFNg30_STAT1 | loaded |
Snyder K562/IFNg6h STAT1 Loaded | 1059 | YDH_K562_IFNg6h_STAT1 | loaded |
Snyder K562/IgG Brg1 Loaded | 893 | YDH_K562_IgG_Brg1 | loaded |
Snyder K562/IgG Control Displayed | 864 | YDH_K562_IgG_Control | loaded |
Snyder K562/IgG Ini1 Loaded | 894 | YDH_K562_IgG_Ini1 | loaded |
Snyder K562/IgG Pol II Loaded | 895 | YDH_K562_IgG_Pol2 | loaded |
Whose?
YHD HeLa S3 BAF155 Displayed | 888 | YDH_HeLa-S3_IgG_BAF155 | loaded |
YHD HeLa S3 BAF170 Loaded | 890 | YDH_HeLa-S3_IgG_BAF170 | loaded |
YHD HeLa S3 Brg1 Loaded | 891 | YDH_HeLa-S3_IgG_Brg1 | loaded |
YHD K562 ATF3 Loaded | 951 | YDH_K562_ATF3 | loaded |
YHD K562 Brf2 Loaded | 1083 | YDH_K562_Brf2 | loaded |
YHD K562 GTF2B Loaded | 975 | YDH_K562_GTF2B | loaded |
YHD K562 NFYB Released
YHD K562 Pol III Displayed
YHD K562 TFIIIC Loaded | 1081 | YDH_K562_TFIIIC | loaded |
YHD K562 NFYA Released
# Work on Farnham's first:
cd {pip}/1088
cp trackDb.ra trackDbCombined.ra
cat ../../900/out/trackDb.ra >> trackDbCombined.ra
cat ../../928/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../900/out/fileDb.ra >> fileDbCombined.ra
cat ../../928/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# convert MNase from treatment to protocol, create SETDB1m=SETDB1_MNase set tags properly
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/1088/out/trackDbCombined.ra trackDb.wgEncode.ra
record wgEncodeYaleChIPseqSignalK562bSetdb1 already exists - use mode=replace
### Big problem: wgEncodeYaleChIPseqSignalK562bSetdb1 was stepped on. Need to revive the table and files!
# current ones on hgwdev should be MNase:
rename table wgEncodeYaleChIPseqSignalK562bSetdb1 to wgEncodeYaleChIPseqSignalK562bSetdb1Mnase;
rename table wgEncodeYaleChIPseqPeaksK562bSetdb1 to wgEncodeYaleChIPseqPeaksK562bSetdb1Mnase;
cd {downloadsDir}
ll release2/*.gz | grep K562bSetdb1
-rw-rw-r-- 1 qateam protein 251376885 Jun 15 2009 release2/wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1.tagAlign.gz
-rw-rw-r-- 1 qateam protein 158487144 Jun 15 2009 release2/wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1.tagAlign.gz
-rw-rw-r-- 1 qateam protein 219694 Jun 15 2009 release2/wgEncodeYaleChIPseqPeaksK562bSetdb1.narrowPeak.gz
-rw-rw-r-- 1 qateam protein 1249353960 Jun 15 2009 release2/wgEncodeYaleChIPseqRawDataRep1K562bSetdb1.fastq.gz
-rw-rw-r-- 1 qateam protein 686668626 Jun 15 2009 release2/wgEncodeYaleChIPseqRawDataRep2K562bSetdb1.fastq.gz
-rw-rw-r-- 1 qateam protein 177107845 Jun 15 2009 release2/wgEncodeYaleChIPseqSignalK562bSetdb1.bedGraph4.gz
[hgwdev:tdreszer wgEncodeYaleChIPseq> ll *.gz | grep K562bSetdb1
-rw-rw-r-- 1 qateam protein 258272496 Jan 16 01:37 wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1.tagAlign.gz
-rw-rw-r-- 1 qateam protein 248369876 Nov 21 19:05 wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 306109438 Jan 16 01:36 wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1.tagAlign.gz
-rw-rw-r-- 1 qateam protein 155170920 Nov 21 17:47 wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 135460 Jan 16 01:20 wgEncodeYaleChIPseqPeaksK562bSetdb1.narrowPeak.gz
-rw-rw-r-- 1 qateam protein 539002203 Jan 16 01:40 wgEncodeYaleChIPseqRawDataRep1K562bSetdb1.fastq.gz
-rw-rw-r-- 1 qateam protein 618070415 Jan 16 01:26 wgEncodeYaleChIPseqRawDataRep2K562bSetdb1.fastq.gz
-rw-rw-r-- 1 qateam protein 198068283 Jan 16 01:33 wgEncodeYaleChIPseqSignalK562bSetdb1.bedGraph4.gz
mv wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1Mnase.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1Mnase.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksK562bSetdb1.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562bSetdb1Mnase.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1K562bSetdb1.fastq.gz wgEncodeYaleChIPseqRawDataRep1K562bSetdb1Mnase.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2K562bSetdb1.fastq.gz wgEncodeYaleChIPseqRawDataRep2K562bSetdb1Mnase.fastq.gz
mv wgEncodeYaleChIPseqSignalK562bSetdb1.bedGraph4.gz wgEncodeYaleChIPseqSignalK562bSetdb1Mnase.bedGraph4.gz
ln release2/wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1.tagAlign.gz .
ln release2/wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1.tagAlign.gz .
ln release2/wgEncodeYaleChIPseqPeaksK562bSetdb1.narrowPeak.gz .
ln release2/wgEncodeYaleChIPseqRawDataRep1K562bSetdb1.fastq.gz .
ln release2/wgEncodeYaleChIPseqRawDataRep2K562bSetdb1.fastq.gz .
ln release2/wgEncodeYaleChIPseqSignalK562bSetdb1.bedGraph4.gz .
e trackDbCombined.ra fileDbCombined.ra
# convert MNase from treatment to protocol, create SETDB1m=SETDB1_MNase set tags properly
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/1088/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
cp fileDb.ra fileDb.ra.2010-01-19
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1088/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
### Note! Somehow the 2nd parm ('.') is now needed!
### Missing tables now: wgEncodeYaleChIPseqSignalK562bSetdb1 & wgEncodeYaleChIPseqPeaksK562bSetdb1
# replace tables from 634? or get them from RR some how?
# Thanks to Erich these are restored.
# Farnham's are done!
/cluster/data/encode/pipeline/bin/encodeStatus.pl 900 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 928 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1088 displayed
### Now start Snyder Mouse_IgG
cd 861/out
cp trackDb.ra trackDbCombined.ra
cat ../../1050/out/trackDb.ra >> trackDbCombined.ra
cat ../../862/out/trackDb.ra >> trackDbCombined.ra
cat ../../956/out/trackDb.ra >> trackDbCombined.ra
cat ../../943/out/trackDb.ra >> trackDbCombined.ra
cat ../../957/out/trackDb.ra >> trackDbCombined.ra
cat ../../863/out/trackDb.ra >> trackDbCombined.ra
cat ../../1051/out/trackDb.ra >> trackDbCombined.ra
cat ../../865/out/trackDb.ra >> trackDbCombined.ra
cat ../../959/out/trackDb.ra >> trackDbCombined.ra
cat ../../941/out/trackDb.ra >> trackDbCombined.ra
cat ../../1008/out/trackDb.ra >> trackDbCombined.ra
cat ../../996/out/trackDb.ra >> trackDbCombined.ra
cat ../../1052/out/trackDb.ra >> trackDbCombined.ra
cat ../../997/out/trackDb.ra >> trackDbCombined.ra
cat ../../1020/out/trackDb.ra >> trackDbCombined.ra
cat ../../945/out/trackDb.ra >> trackDbCombined.ra
cat ../../1016/out/trackDb.ra >> trackDbCombined.ra
cat ../../1025/out/trackDb.ra >> trackDbCombined.ra
cat ../../942/out/trackDb.ra >> trackDbCombined.ra
cat ../../1024/out/trackDb.ra >> trackDbCombined.ra
cat ../../1044/out/trackDb.ra >> trackDbCombined.ra
cat ../../1053/out/trackDb.ra >> trackDbCombined.ra
cat ../../1029/out/trackDb.ra >> trackDbCombined.ra
cat ../../1045/out/trackDb.ra >> trackDbCombined.ra
cat ../../946/out/trackDb.ra >> trackDbCombined.ra
cat ../../1046/out/trackDb.ra >> trackDbCombined.ra
cat ../../1047/out/trackDb.ra >> trackDbCombined.ra
cat ../../947/out/trackDb.ra >> trackDbCombined.ra
cat ../../1048/out/trackDb.ra >> trackDbCombined.ra
cat ../../893/out/trackDb.ra >> trackDbCombined.ra
cat ../../864/out/trackDb.ra >> trackDbCombined.ra
cat ../../894/out/trackDb.ra >> trackDbCombined.ra
cat ../../895/out/trackDb.ra >> trackDbCombined.ra
cat ../../892/out/trackDb.ra >> trackDbCombined.ra
cat ../../999/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../1050/out/fileDb.ra >> fileDbCombined.ra
cat ../../862/out/fileDb.ra >> fileDbCombined.ra
cat ../../956/out/fileDb.ra >> fileDbCombined.ra
cat ../../943/out/fileDb.ra >> fileDbCombined.ra
cat ../../957/out/fileDb.ra >> fileDbCombined.ra
cat ../../863/out/fileDb.ra >> fileDbCombined.ra
cat ../../1051/out/fileDb.ra >> fileDbCombined.ra
cat ../../865/out/fileDb.ra >> fileDbCombined.ra
cat ../../959/out/fileDb.ra >> fileDbCombined.ra
cat ../../941/out/fileDb.ra >> fileDbCombined.ra
cat ../../1008/out/fileDb.ra >> fileDbCombined.ra
cat ../../996/out/fileDb.ra >> fileDbCombined.ra
cat ../../1052/out/fileDb.ra >> fileDbCombined.ra
cat ../../997/out/fileDb.ra >> fileDbCombined.ra
cat ../../1020/out/fileDb.ra >> fileDbCombined.ra
cat ../../945/out/fileDb.ra >> fileDbCombined.ra
cat ../../1016/out/fileDb.ra >> fileDbCombined.ra
cat ../../1025/out/fileDb.ra >> fileDbCombined.ra
cat ../../942/out/fileDb.ra >> fileDbCombined.ra
cat ../../1024/out/fileDb.ra >> fileDbCombined.ra
cat ../../1044/out/fileDb.ra >> fileDbCombined.ra
cat ../../1053/out/fileDb.ra >> fileDbCombined.ra
cat ../../1029/out/fileDb.ra >> fileDbCombined.ra
cat ../../1045/out/fileDb.ra >> fileDbCombined.ra
cat ../../946/out/fileDb.ra >> fileDbCombined.ra
cat ../../1046/out/fileDb.ra >> fileDbCombined.ra
cat ../../1047/out/fileDb.ra >> fileDbCombined.ra
cat ../../947/out/fileDb.ra >> fileDbCombined.ra
cat ../../1048/out/fileDb.ra >> fileDbCombined.ra
cat ../../893/out/fileDb.ra >> fileDbCombined.ra
cat ../../864/out/fileDb.ra >> fileDbCombined.ra
cat ../../894/out/fileDb.ra >> fileDbCombined.ra
cat ../../895/out/fileDb.ra >> fileDbCombined.ra
cat ../../892/out/fileDb.ra >> fileDbCombined.ra
cat ../../999/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# Edit for protocol, Brg1mig Ini1mig NRF1mig NFKBmig Pol2mig, GM12892 GM15510 GM15510 GM18505 GM18526 GM18951 GM19099 GM19193 Stanford(Snyder)
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 861 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1050 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 862 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 956 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 943 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 957 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 863 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1051 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 865 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 959 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 941 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1008 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 996 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1052 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 997 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1020 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 945 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1016 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1025 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 942 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1024 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1044 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1053 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1029 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1045 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 946 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1046 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1047 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 947 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1048 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 893 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 864 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 894 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 895 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 892 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 999 displayed
# Done with Snyder Mouse_IgG
### Now start Snyder Rabbit_IgG
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/861/out/trackDbCombined.ra trackDb.wgEncode.ra
cd ../../1030/out
cp trackDb.ra trackDbCombined.ra
cat ../../1031/out/trackDb.ra >> trackDbCombined.ra
cat ../../1032/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../1031/out/fileDb.ra >> fileDbCombined.ra
cat ../../1032/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# Edit for protocol CJUNrig JUNDrig yIGGrab
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1030/out/trackDbCombined.ra trackDb.wgEncode.ra
### Ouch. Table names need changing:
rename table wgEncodeYaleChIPseqSignalHelas3Cjun to wgEncodeYaleChIPseqSignalHelas3CjunRabigg;
rename table wgEncodeYaleChIPseqPeaksHelas3Cjun to wgEncodeYaleChIPseqPeaksHelas3CjunRabigg;
rename table wgEncodeYaleChIPseqSignalHelas3Jund to wgEncodeYaleChIPseqSignalHelas3JundRabigg;
rename table wgEncodeYaleChIPseqPeaksHelas3Jund to wgEncodeYaleChIPseqPeaksHelas3JundRabigg;
mv wgEncodeYaleChIPseqAlignmentsRep1Helas3Jund.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Helas3JundRabigg.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Helas3Jund.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Helas3JundRabigg.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksHelas3Jund.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3JundRabigg.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1Helas3Jund.fastq.gz wgEncodeYaleChIPseqRawDataRep1Helas3JundRabigg.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Helas3Jund.fastq.gz wgEncodeYaleChIPseqRawDataRep2Helas3JundRabigg.fastq.gz
mv wgEncodeYaleChIPseqSignalHelas3Jund.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3JundRabigg.bedGraph4.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Helas3Cjun.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Helas3CjunRabigg.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Helas3Cjun.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Helas3CjunRabigg.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksHelas3Cjun.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3CjunRabigg.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1Helas3Cjun.fastq.gz wgEncodeYaleChIPseqRawDataRep1Helas3CjunRabigg.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Helas3Cjun.fastq.gz wgEncodeYaleChIPseqRawDataRep2Helas3CjunRabigg.fastq.gz
mv wgEncodeYaleChIPseqSignalHelas3Cjun.bedGraph4.gz wgEncodeYaleChIPseqSignalHelas3CjunRabigg.bedGraph4.gz
e trackDbCombined.ra fileDbCombined.ra
# Edit for file/table name changes
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1030/out/trackDbCombined.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/1030/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1030/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1030 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1031 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1032 displayed
# Done with Snyder Rabbit_IgG
### Now start Snyder Insulin and Forkskolin
cd ../../1070/out
cp trackDb.ra trackDbCombined.ra
cat ../../1073/out/trackDb.ra >> trackDbCombined.ra
cat ../../1066/out/trackDb.ra >> trackDbCombined.ra
cat ../../1069/out/trackDb.ra >> trackDbCombined.ra
cat ../../1063/out/trackDb.ra >> trackDbCombined.ra
cat ../../1068/out/trackDb.ra >> trackDbCombined.ra
cat ../../1072/out/trackDb.ra >> trackDbCombined.ra
cat ../../1071/out/trackDb.ra >> trackDbCombined.ra
cat ../../1062/out/trackDb.ra >> trackDbCombined.ra
cat ../../1067/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../1073/out/fileDb.ra >> fileDbCombined.ra
cat ../../1066/out/fileDb.ra >> fileDbCombined.ra
cat ../../1069/out/fileDb.ra >> fileDbCombined.ra
cat ../../1063/out/fileDb.ra >> fileDbCombined.ra
cat ../../1068/out/fileDb.ra >> fileDbCombined.ra
cat ../../1072/out/fileDb.ra >> fileDbCombined.ra
cat ../../1071/out/fileDb.ra >> fileDbCombined.ra
cat ../../1062/out/fileDb.ra >> fileDbCombined.ra
cat ../../1067/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# Edit for forskolin, insulin uHEPG2for, uHEPG2for, HSF1, ERRA, HNF4A, PGC1A, CEBPB, GRP20
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1070/out/trackDbCombined.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/1070/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1070/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1070 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1073 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1066 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1069 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1063 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1068 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1072 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1071 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1062 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1067 displayed
# Done with Snyder Forskolin and Insulin
### Now get 3 more IgGs
cd ../../888/out
cp trackDb.ra trackDbCombined.ra
cat ../../890/out/trackDb.ra >> trackDbCombined.ra
cat ../../891/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../890/out/fileDb.ra >> fileDbCombined.ra
cat ../../891/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# edit for BAF155mig, BAF170mig, BRG1mig, protocol=MUSIGG,
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/888/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/888/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 888 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 890 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 891 displayed
# Done with 3 more IgGs
### Now get 3 IFNs
cd ../../974/out
cp trackDb.ra trackDbCombined.ra
cat ../../1058/out/trackDb.ra >> trackDbCombined.ra
cat ../../1059/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../1058/out/fileDb.ra >> fileDbCombined.ra
cat ../../1059/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
## Clean up:
drop table wgEncodeYaleChIPseqRawSignalRep1K562Ifng30Pol2;
drop table wgEncodeYaleChIPseqRawSignalRep2K562Ifng30Pol2;
rm /gbdb/hg18/wib/wgEncodeYaleChIPseqRawSignalRep1K562Ifng30Pol2.wib
rm /gbdb/hg18/wib/wgEncodeYaleChIPseqRawSignalRep2K562Ifng30Pol2.wib
rename table wgEncodeYaleChIPseqSignalK562Stat1 to wgEncodeYaleChIPseqSignalK562Stat1Ifng6h;
rename table wgEncodeYaleChIPseqPeaksK562Stat1 to wgEncodeYaleChIPseqPeaksK562Stat1Ifng6h;
mv wgEncodeYaleChIPseqAlignmentsRep1K562Stat1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1K562Stat1Ifng6h.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2K562Stat1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2K562Stat1Ifng6h.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksK562Stat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562Stat1Ifng6h.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1K562Stat1.fastq.gz wgEncodeYaleChIPseqRawDataRep1K562Stat1Ifng6h.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2K562Stat1.fastq.gz wgEncodeYaleChIPseqRawDataRep2K562Stat1Ifng6h.fastq.gz
mv wgEncodeYaleChIPseqSignalK562Stat1.bedGraph4.gz wgEncodeYaleChIPseqSignalK562Stat1Ifng6h.bedGraph4.gz
# edit for Name change uK562Ig30, uK562Ig6, treatment
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/974/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/974/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 974 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1058 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1059 displayed
# Done with 3 IFNs
### Now get 4 misc. for Snyder
cd ../../950/out
cp trackDb.ra trackDbCombined.ra
cat ../../995/out/trackDb.ra >> trackDbCombined.ra
cat ../../1085/out/trackDb.ra >> trackDbCombined.ra
cat ../../1076/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../995/out/fileDb.ra >> fileDbCombined.ra
cat ../../1085/out/fileDb.ra >> fileDbCombined.ra
cat ../../1076/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# edit for tags
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/950/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/950/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 950 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 995 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1085 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1076 displayed
# Done with 4 misc. for Snyder
### Now start 7 for Struhl
cd ../../933/out
cp trackDb.ra trackDbCombined.ra
cat ../../952/out/trackDb.ra >> trackDbCombined.ra
cat ../../1078/out/trackDb.ra >> trackDbCombined.ra
cat ../../1086/out/trackDb.ra >> trackDbCombined.ra
cat ../../1087/out/trackDb.ra >> trackDbCombined.ra
cat ../../1082/out/trackDb.ra >> trackDbCombined.ra
cat ../../1077/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../952/out/fileDb.ra >> fileDbCombined.ra
cat ../../1078/out/fileDb.ra >> fileDbCombined.ra
cat ../../1086/out/fileDb.ra >> fileDbCombined.ra
cat ../../1087/out/fileDb.ra >> fileDbCombined.ra
cat ../../1082/out/fileDb.ra >> fileDbCombined.ra
cat ../../1077/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# edit for tags, Struhl, ZZZ3, NELFE, BRF2, TFIIIC
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/933/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/933/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 933 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 952 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1078 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1086 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1087 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1082 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1077 displayed
# Done with 7 for Struhl
### Now start last 4 (for Struhl)
cd ../../951/out
cp trackDb.ra trackDbCombined.ra
cat ../../975/out/trackDb.ra >> trackDbCombined.ra
cat ../../1083/out/trackDb.ra >> trackDbCombined.ra
cat ../../1081/out/trackDb.ra >> trackDbCombined.ra
cp fileDb.ra fileDbCombined.ra
cat ../../975/out/fileDb.ra >> fileDbCombined.ra
cat ../../1083/out/fileDb.ra >> fileDbCombined.ra
cat ../../1081/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra
# edit for tags, Struhl, ATF3, GTF2B
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/951/out/trackDbCombined.ra trackDb.wgEncode.ra
cvs ci
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/951/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 951 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 975 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1083 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1081 displayed
### Now there are a loage number of files in the downloads dir without metadata. Are these from unloaded submissions (correcting protocol)?
# These were all left overs from correcting protocol submissions:
ll *.gz | grep Gm12878Musigg
ls wgEncodeYaleChIPseq*Gm12878Musigg.*
rm wgEncodeYaleChIPseq*Gm12878Musigg.*
ll *.gz | grep Gm12878Nfkb
ls wgEncodeYaleChIPseq*Gm12878Nfkb.*
rm wgEncodeYaleChIPseq*Gm12878Nfkb.*
ll *.gz | grep Gm12891Pol2
ll wgEncodeYaleChIPseq*Gm12891Pol2.*
rm wgEncodeYaleChIPseq*Gm12891Pol2.*
ll *.gz | grep Gm12892Musigg
ll wgEncodeYaleChIPseq*Gm12892Musigg.*
rm wgEncodeYaleChIPseq*Gm12892Musigg.*
ll *.gz | grep Gm12892Nfkb
ll wgEncodeYaleChIPseq*Gm12892Nfkb.*
rm wgEncodeYaleChIPseq*Gm12892Nfkb.*
ll *.gz | grep Gm12892Pol2
ll wgEncodeYaleChIPseq*Gm12892Pol2.*
rm wgEncodeYaleChIPseq*Gm12892Pol2.*
ll *.gz | grep Gm15510Musigg
ll wgEncodeYaleChIPseq*Gm15510Musigg.*
rm wgEncodeYaleChIPseq*Gm15510Musigg.*
ll *.gz | grep Gm15510Pol2
ll wgEncodeYaleChIPseq*Gm15510Pol2.*
rm wgEncodeYaleChIPseq*Gm15510Pol2.*
ll *.gz | grep Gm18505Nfkb
ll wgEncodeYaleChIPseq*Gm18505Nfkb.*
rm wgEncodeYaleChIPseq*Gm18505Nfkb.*
ll *.gz | grep Gm18505Pol2
ll wgEncodeYaleChIPseq*Gm18505Pol2.*
rm wgEncodeYaleChIPseq*Gm18505Pol2.*
ll *.gz | grep Gm18526Nfkb
ll wgEncodeYaleChIPseq*Gm18526Nfkb.*
rm wgEncodeYaleChIPseq*Gm18526Nfkb.*
ll *.gz | grep Gm18526Pol2
ll wgEncodeYaleChIPseq*Gm18526Pol2.*
rm wgEncodeYaleChIPseq*Gm18526Pol2.*
ll *.gz | grep Gm18951Pol2
ll wgEncodeYaleChIPseq*Gm18951Pol2.*
rm wgEncodeYaleChIPseq*Gm18951Pol2.*
ll *.gz | grep Gm19099Nfkb
ll wgEncodeYaleChIPseq*Gm19099Nfkb.*
rm wgEncodeYaleChIPseq*Gm19099Nfkb.*
ll *.gz | grep Gm19193Nfkb
ll wgEncodeYaleChIPseq*Gm19193Nfkb.*
rm wgEncodeYaleChIPseq*Gm19193Nfkb.*
ll *.gz | grep Helas3Baf170
ll wgEncodeYaleChIPseq*Helas3Baf170.*
rm wgEncodeYaleChIPseq*Helas3Baf170.*
ll *.gz | grep Helas3Brg1
ll wgEncodeYaleChIPseq*Helas3Brg1.*
rm wgEncodeYaleChIPseq*Helas3Brg1.*
ll *.gz | grep Helas3Ini1
ll wgEncodeYaleChIPseq*Helas3Ini1.*
rm wgEncodeYaleChIPseq*Helas3Ini1.*
ll *.gz | grep K562Brg1
ll wgEncodeYaleChIPseq*K562Brg1.*
rm wgEncodeYaleChIPseq*K562Brg1.*
ll *.gz | grep K562Ini1
ll wgEncodeYaleChIPseq*K562Ini1.*
rm wgEncodeYaleChIPseq*K562Ini1.*
ll *.gz | grep K562Pol2 | grep Jan
ll wgEncodeYaleChIPseq*K562Pol2.*
rm wgEncodeYaleChIPseqAlignmentsRep1K562Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Pol2.tagAlign.gz
rm wgEncodeYaleChIPseqPeaksK562Pol2.narrowPeak.gz
rm wgEncodeYaleChIPseqRawDataRep1K562Pol2.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep2K562Pol2.fastq.gz
rm wgEncodeYaleChIPseqSignalK562Pol2.bedGraph4.gz
ll *.gz | grep K562bSetdb1
# old refuse. Nothing stepped on
rm wgEncodeYaleChIPseqAlignmentsRep1K562bSetdb1.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562bSetdb1.tagAlign.gz
# fileDb.ra editing problems:
wgEncodeYaleChIPseqAlignmentsRep1Helas3CjunRabigg.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep1K562Stat1Ifng6h.tagAlign.gz
# This one is a mess. It looks like HeLaMouseIgG from Feb 2009 was stepped on. However much of this should have been V2
wgEncodeYaleChIPseqAlignmentsRep1Helas3Mouseigg.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2Helas3Mouseigg.tagAlign.gz
wgEncodeYaleChIPseqSignalHelas3Mouseigg.bedGraph4.gz
ll *.gz | grep Helas3Mouseigg
ll *.gz | grep wgEncodeYaleChIPseqAlignmentsRep1Helas3 | grep igg
# stepped on
-rw-rw-r-- 1 qateam protein 407130754 Jan 5 23:30 wgEncodeYaleChIPseqRawDataRep1Helas3Mouseigg.fastq.gz
-rw-rw-r-- 1 qateam protein 442269812 Jan 5 23:34 wgEncodeYaleChIPseqRawDataRep2Helas3Mouseigg.fastq.gz
ll release1/wgEncodeYaleChIPseqRawDataRep1Helas3Mouseigg.fastq.gz
ll release1/wgEncodeYaleChIPseqRawDataRep2Helas3Mouseigg.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep1Helas3Mouseigg.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep2Helas3Mouseigg.fastq.gz
ln release1/wgEncodeYaleChIPseqRawDataRep1Helas3Mouseigg.fastq.gz .
ln release1/wgEncodeYaleChIPseqRawDataRep2Helas3Mouseigg.fastq.gz .
# Would have stepped on except no collision because of V2:
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqSignalHelas3Mouseigg.bedGraph4.gz
encodeDownloadsPage.pl index.html .
### Done for now on getting all of Yale's Jan 2010 freeze submissions displayed!
2010-01-21 Stealph loading of one more submission
=================================================
Mike Wilson uploaded to ftp dir
I created new submission, then assigned it to him
mkdir {pip}/1090
cd 1090
mv ../../ftp/prod/mpw6/MCF-7_Input.tgz 001_MCF-7_Input.tgz
tar -xzf 001_MCF-7_Input.tgz &
# load through the pipeline
make alpha DBS=hg18
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1090/out/fileDb.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1090 displayed
hg18.wgEncodeYaleChIPseqSignalGm10847Input has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm10847MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm10847NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm10847Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm10847Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Nfkb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Rad21 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Tr4 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Yy1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Zzz3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891Mouseigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892Nfkb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18505MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18505Nfkb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18505NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18505Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526Nfkb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18951NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18951Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19099MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19099Nfkb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19099NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19193MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19193Nfkb has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19193NfkbMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19193Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Baf155 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Baf155Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Baf170 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Baf170Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Bdp1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Brf2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Brg1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Brg1Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3E2f1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Ini1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Ini1Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Jund has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Mouseigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Nrf1Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Rabigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHelas3Rpc155 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2CebpbForskln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2ControlForskln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2ControlInsln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2ErraForskln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2Hsf1Forskln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2Pgc1aForskln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHepg2Srebp1aInsln has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHuvecCjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHuvecMax has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalHuvecPol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Atf3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Brf2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Brg1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Brg1Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ifng30Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ini1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Ini1Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Mouseigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562MusiggMusigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Nelfe has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Pol2 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Pol2Musigg has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Stat1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Stat1Ifng30 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562Tfiiic has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalK562bSetdb1 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalMcf7Input has 1 records with end > chromSize.
update wgEncodeYaleChIPseqSignalGm12891Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm12892MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm12892NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm12892Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm15510MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm15510NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm15510Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18505MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18505NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18505Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18526MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18526NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18526Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18951NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18951Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19099MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19099NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19193MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19193NfkbMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19193Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Baf155Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Baf170Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Bdp1 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Brf2 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Brg1Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3E2f1 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Ini1Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Jund y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
# error, doesn't exist
update wgEncodeYaleChIPseqSignalHelas3Mouseigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
# error, doesn't exist
update wgEncodeYaleChIPseqSignalHelas3Nrf1Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Rabigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Rpc155 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2CebpbForskln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2ControlForskln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2ControlInsln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2ErraForskln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2Hsf1Forskln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2Pgc1aForskln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHepg2Srebp1aInsln y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHuvecCjun y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHuvecMax y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHuvecPol2 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Atf3 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Brf2 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Brg1Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Ifng30Pol2 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Ini1Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562MusiggMusigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Nelfe y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Pol2Musigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Stat1 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
# error, doesn't exist
update wgEncodeYaleChIPseqSignalK562Stat1Ifng30 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Tfiiic y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562bSetdb1 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalMcf7Input y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
# created cleanUp.txt in downloads dir
hgsql hg18 < cleanUp.txt > cleanUp.log &
psg 6905
tdreszer 6905 32116 0 17:25 pts/15 00:00:00 mysql -u hgcat -px xxxxxxxxx -hlocalhost -A hg18
top
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
8177 mysql 15 0 4995m 3.3g 3828 S 183 1.3 1287:36 mysqld
# I think it is running but I don't see any output.
# error on missing table. edit cleanUp.txt and
hgsql hg18 < cleanUp.txt > cleanUp.log &
psg 24689
tdreszer 24689 32116 0 18:10 pts/15 00:00:00 mysql -u hgcat -px xxxxxxxxx -hlocalhost -A hg18
# error on missing table. edit cleanUp.txt and
hgsql hg18 < cleanUp.txt > cleanUp.log &
psg 30066
tdreszer 30066 32116 0 19:37 pts/15 00:00:00 mysql -u hgcat -px xxxxxxxxx -hlocalhost -A hg18
[1]+ Done hgsql hg18 < cleanUp.txt > cleanUp.log
## At the freeze:
select id,name,status,user_id,created_at from projects where status = "displayed" and user_id = 6 and created_at > date('2009-12-01') order by name;
+------+--------------------------------+-----------+---------+---------------------+
| id | name | status | user_id | created_at |
+------+--------------------------------+-----------+---------+---------------------+
| 861 | YDH_GM10847_IgG_Control | displayed | 6 | 2009-12-20 20:42:24 |
| 1050 | YDH_GM10847_IgG_NFKB | displayed | 6 | 2010-01-13 23:58:01 |
| 862 | YDH_GM10847_IgG_Pol2 | displayed | 6 | 2009-12-20 20:42:33 |
| 956 | YDH_GM12878_IgG_Control | displayed | 6 | 2010-01-09 11:02:38 |
| 943 | YDH_GM12878_IgG_NFKB | displayed | 6 | 2010-01-08 19:33:23 |
| 957 | YDH_GM12878_IgG_Pol2 | displayed | 6 | 2010-01-09 12:43:01 |
| 1076 | YDH_GM12878_Rad21 | displayed | 6 | 2010-01-15 09:54:47 |
| 900 | YDH_GM12878_TR4 | displayed | 6 | 2010-01-06 12:18:31 |
| 853 | YDH_GM12878_YY1 | displayed | 6 | 2009-12-19 17:45:56 |
| 933 | YDH_GM12878_ZZZ3 | displayed | 6 | 2010-01-08 08:19:09 |
| 863 | YDH_GM12891_IgG_Control | displayed | 6 | 2009-12-20 21:36:36 |
| 1051 | YDH_GM12891_IgG_NFKB | displayed | 6 | 2010-01-13 23:58:13 |
| 865 | YDH_GM12891_IgG_Pol2 | displayed | 6 | 2009-12-22 08:47:06 |
| 959 | YDH_GM12892_IgG_Control | displayed | 6 | 2010-01-09 13:34:23 |
| 941 | YDH_GM12892_IgG_NFKB | displayed | 6 | 2010-01-08 19:29:02 |
| 1008 | YDH_GM12892_IgG_Pol2 | displayed | 6 | 2010-01-12 17:38:28 |
| 996 | YDH_GM15510_IgG_Control | displayed | 6 | 2010-01-11 19:56:53 |
| 1052 | YDH_GM15510_IgG_NFKB | displayed | 6 | 2010-01-13 23:58:26 |
| 997 | YDH_GM15510_IgG_Pol2 | displayed | 6 | 2010-01-11 19:57:02 |
| 945 | YDH_GM18505_IgG_NFKB | displayed | 6 | 2010-01-08 19:48:25 |
| 1016 | YDH_GM18505_IgG_Pol2 | displayed | 6 | 2010-01-13 03:11:16 |
| 1025 | YDH_GM18526_IgG_Control | displayed | 6 | 2010-01-13 07:49:24 |
| 942 | YDH_GM18526_IgG_NFKB | displayed | 6 | 2010-01-08 19:30:22 |
| 1024 | YDH_GM18526_IgG_Pol2 | displayed | 6 | 2010-01-13 07:38:50 |
| 1044 | YDH_GM18951_IgG_Control | displayed | 6 | 2010-01-13 23:15:38 |
| 1053 | YDH_GM18951_IgG_NFKB | displayed | 6 | 2010-01-13 23:58:37 |
| 1029 | YDH_GM18951_IgG_Pol2 | displayed | 6 | 2010-01-13 11:52:57 |
| 1045 | YDH_GM19099_IgG_Control | displayed | 6 | 2010-01-13 23:15:58 |
| 946 | YDH_GM19099_IgG_NFKB | displayed | 6 | 2010-01-08 19:48:47 |
| 1046 | YDH_GM19099_IgG_Pol2 | displayed | 6 | 2010-01-13 23:16:09 |
| 1047 | YDH_GM19193_IgG_Control | displayed | 6 | 2010-01-13 23:16:28 |
| 947 | YDH_GM19193_IgG_NFKB | displayed | 6 | 2010-01-08 19:49:49 |
| 1048 | YDH_GM19193_IgG_Pol2 | displayed | 6 | 2010-01-13 23:16:47 |
| 1078 | YDH_HeLa-S3_Bdp1 | displayed | 6 | 2010-01-15 13:13:41 |
| 1086 | YDH_HeLa-S3_Brf1 | displayed | 6 | 2010-01-15 16:39:05 |
| 1087 | YDH_HeLa-S3_Brf2 | displayed | 6 | 2010-01-15 16:39:16 |
| 928 | YDH_HeLa-S3_E2F1 | displayed | 6 | 2010-01-08 04:23:27 |
| 888 | YDH_HeLa-S3_IgG_BAF155 | displayed | 6 | 2010-01-05 12:54:58 |
| 890 | YDH_HeLa-S3_IgG_BAF170 | displayed | 6 | 2010-01-05 12:55:48 |
| 891 | YDH_HeLa-S3_IgG_Brg1 | displayed | 6 | 2010-01-05 12:56:06 |
| 892 | YDH_HeLa-S3_IgG_Ini1 | displayed | 6 | 2010-01-05 12:56:20 |
| 999 | YDH_HeLa-S3_IgG_Nrf1 | displayed | 6 | 2010-01-12 06:39:47 |
| 1031 | YDH_HeLa-S3_IgG_Rabbit_c-Jun | displayed | 6 | 2010-01-13 12:52:46 |
| 1030 | YDH_HeLa-S3_IgG_Rabbit_Control | displayed | 6 | 2010-01-13 12:52:27 |
| 1032 | YDH_HeLa-S3_IgG_Rabbit_JunD | displayed | 6 | 2010-01-13 12:53:07 |
| 1082 | YDH_HeLa-S3_RPC155 | displayed | 6 | 2010-01-15 15:19:58 |
| 1077 | YDH_HeLa-S3_TFIIIC | displayed | 6 | 2010-01-15 12:13:48 |
| 1062 | YDH_HepG2_Forskolin_CEBPB | displayed | 6 | 2010-01-14 21:03:30 |
| 995 | YDH_HUVEC_Jun | displayed | 6 | 2010-01-11 17:20:20 |
| 1085 | YDH_HUVEC_Max | displayed | 6 | 2010-01-15 16:38:48 |
| 950 | YDH_HUVEC_Pol2 | displayed | 6 | 2010-01-08 22:51:27 |
| 1088 | YDH_K562b_MNase_SetDB1 | displayed | 6 | 2010-01-15 16:40:28 |
| 860 | YDH_K562b_ZNF274 | displayed | 6 | 2009-12-20 20:02:55 |
| 951 | YDH_K562_ATF3 | displayed | 6 | 2010-01-08 23:27:47 |
| 1083 | YDH_K562_Brf2 | displayed | 6 | 2010-01-15 15:29:52 |
| 975 | YDH_K562_GTF2B | displayed | 6 | 2010-01-11 11:54:17 |
| 974 | YDH_K562_IFNg30_Pol2 | displayed | 6 | 2010-01-11 08:56:39 |
| 1058 | YDH_K562_IFNg30_STAT1 | displayed | 6 | 2010-01-14 18:29:56 |
| 1059 | YDH_K562_IFNg6h_STAT1 | displayed | 6 | 2010-01-14 19:32:38 |
| 893 | YDH_K562_IgG_Brg1 | displayed | 6 | 2010-01-05 13:31:54 |
| 864 | YDH_K562_IgG_Control | displayed | 6 | 2009-12-21 14:27:16 |
| 894 | YDH_K562_IgG_Ini1 | displayed | 6 | 2010-01-05 13:32:13 |
| 895 | YDH_K562_IgG_Pol2 | displayed | 6 | 2010-01-05 13:32:22 |
| 952 | YDH_K562_NELFe | displayed | 6 | 2010-01-08 23:28:03 |
| 1081 | YDH_K562_TFIIIC | displayed | 6 | 2010-01-15 15:07:40 |
| 1090 | YDH_MCF-7_Input | displayed | 6 | 2010-01-21 13:13:23 |
| 1020 | YHD_GM18505_IgG_Control | displayed | 6 | 2010-01-13 07:15:07 |
| 1066 | YHD_HepG2_Forskolin_Control | displayed | 6 | 2010-01-14 21:17:40 |
| 1063 | YHD_HepG2_Forskolin_ERRA | displayed | 6 | 2010-01-14 21:15:31 |
| 1067 | YHD_HepG2_Forskolin_GRp20 | displayed | 6 | 2010-01-14 21:18:02 |
| 1068 | YHD_HepG2_Forskolin_HNF4A | displayed | 6 | 2010-01-14 21:18:21 |
| 1069 | YHD_HepG2_Forskolin_HSF1 | displayed | 6 | 2010-01-14 21:18:49 |
| 1071 | YHD_HepG2_Forskolin_PGC1A | displayed | 6 | 2010-01-14 21:19:35 |
| 1072 | YHD_HepG2_Forskolin_Pol2 | displayed | 6 | 2010-01-14 21:19:56 |
| 1070 | YHD_HepG2_Insulin_Control | displayed | 6 | 2010-01-14 21:19:10 |
| 1073 | YHD_HepG2_Insulin_SREBP1 | displayed | 6 | 2010-01-14 21:20:30 |
+------+--------------------------------+-----------+---------+---------------------+
76 rows
### Post call problems:
1) ZZZ3 described as ZZ3 in cv.ra FIXED
2) NF-YB is decribed as NF-YA in cv.ra FIXED
3) TFIIIC need to be converted to TFIIIC-110 in cv.ra and metadata FIXED
4) SREBP1A becomes SREBP1 FIXED
5) Need new treatment pravastatin DONE
6) HepG2/SREBP1 becomes HepG2/SREBP1/pravastatin DONE
7) Need to move 3 more from HepG2 to HepG2/pravastatin
8) Need to move HepG2/input to HepG2/input/pravastatin
9) Leaves 14 datasetts in question:
GM12878/Rad21/rabIgGb Formerly paired with standard Input
GM12878/NFKB/rabIgG Formerly paired with musIgG, but rabbit is the appropriate choice
GM10847/NFKB/rabIgG "
GM12891/NFKB/rabIgG "
GM12892/NFKB/rabIgG "
GM15510/NFKB/rabIgG "
GM18505/NFKB/rabIgG "
GM18526/NFKB/rabIgG "
GM18951/NFKB/rabIgG "
GM19099/NFKB/rabIgG "
GM19193/NFKB/rabIgG "
HUVEC/c-Jun No Input for HUVEC ever submitted
HUVEC/Max No Input for HUVEC ever submitted
HUVEC/Pol2 No Input for HUVEC ever submitted
### GMs will be paired with iGGmus: edit trackDb and fileDb metadata
### HUVEC must be revoked
### Duplicate fastqs!
ll wgEncodeYaleChIPseq*Gm12878Pol2Musigg.fastq.*
-rw-rw-r-- 1 qateam protein 170335911 Jan 12 14:57 wgEncodeYaleChIPseqRawDataRep1Gm12878Pol2Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 188279133 Jan 12 14:33 wgEncodeYaleChIPseqRawDataRep2Gm12878Pol2Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 167890919 Jan 12 15:08 wgEncodeYaleChIPseqRawDataRep3Gm12878Pol2Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 167890919 Jan 12 14:36 wgEncodeYaleChIPseqRawDataRep4Gm12878Pol2Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 167890919 Jan 12 14:54 wgEncodeYaleChIPseqRawDataRep5Gm12878Pol2Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 167890919 Jan 12 15:05 wgEncodeYaleChIPseqRawDataRep6Gm12878Pol2Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 167890919 Jan 12 15:06 wgEncodeYaleChIPseqRawDataRep7Gm12878Pol2Musigg.fastq.gz
zdiff wgEncodeYaleChIPseqRawDataRep3Gm12878Pol2Musigg.fastq.gz wgEncodeYaleChIPseqRawDataRep4Gm12878Pol2Musigg.fastq.gz
>> identical
m *.DDF
files view cell antibody protocol replicate labVersion
data/GM12878_IgG_Pol2_sequence_rep1*.fastq RawData GM12878 Pol2 Mouse_IgG 1 Illumina
data/GM12878_IgG_Pol2_sequence_rep2*.fastq RawData GM12878 Pol2 Mouse_IgG 2 Illumina
data/GM12878_IgG_Pol2_sequence_rep3*.fastq RawData GM12878 Pol2 Mouse_IgG 3 Illumina
data/GM12878_IgG_Pol2_sequence_rep3*.fastq RawData GM12878 Pol2 Mouse_IgG 4 Illumina
data/GM12878_IgG_Pol2_sequence_rep3*.fastq RawData GM12878 Pol2 Mouse_IgG 5 Data pair
data/GM12878_IgG_Pol2_sequence_rep3*.fastq RawData GM12878 Pol2 Mouse_IgG 6 Illumina
data/GM12878_IgG_Pol2_sequence_rep3*.fastq RawData GM12878 Pol2 Mouse_IgG 7 Illumina
ls data/*sequence_*
data/GM12878_IgG_Pol2_sequence_rep1_FC30V1RHM_20081223_s_5.fastq
data/GM12878_IgG_Pol2_sequence_rep2_FC30V1RHM_20081223_s_6.fastq
data/GM12878_IgG_Pol2_sequence_rep3_FC30V1RHM_20081223_s_8.fastq
data/GM12878_IgG_Pol2_sequence_rep4_FC30WBTHM_20090123_s_6.fastq
data/GM12878_IgG_Pol2_sequence_rep5_FC42PUHM_20090706_s_3.fastq
data/GM12878_IgG_Pol2_sequence_rep6_laneA_FC201BPAA_032708_s_7.fastq
data/GM12878_IgG_Pol2_sequence_rep6_laneB_FC201BPAA_032708_s_8.fastq
data/GM12878_IgG_Pol2_sequence_rep7_laneA_FC20698AA_031908_s_5.fastq
data/GM12878_IgG_Pol2_sequence_rep7_laneB_FC20698AA_031908_s_6.fastq
/bin/gzip -c data/GM12878_IgG_Pol2_sequence_rep4_FC30WBTHM_20090123_s_6.fastq > /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep4Gm12878Pol2Musigg.fastq.gz
/bin/gzip -c data/GM12878_IgG_Pol2_sequence_rep5_FC42PUHM_20090706_s_3.fastq > /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqRawDataRep5Gm12878Pol2Musigg.fastq.gz
cp data/GM12878_IgG_Pol2_sequence_rep6_laneA_FC201BPAA_032708_s_7.fastq wgEncodeYaleChIPseqRawDataRep6Gm12878Pol2Musigg.fastq
cat data/GM12878_IgG_Pol2_sequence_rep6_laneB_FC201BPAA_032708_s_8.fastq >> wgEncodeYaleChIPseqRawDataRep6Gm12878Pol2Musigg.fastq
/bin/gzip wgEncodeYaleChIPseqRawDataRep6Gm12878Pol2Musigg.fastq
mv wgEncodeYaleChIPseqRawDataRep6Gm12878Pol2Musigg.fastq.gz /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/
cp data/GM12878_IgG_Pol2_sequence_rep7_laneA_FC20698AA_031908_s_5.fastq wgEncodeYaleChIPseqRawDataRep7Gm12878Pol2Musigg.fastq
cat data/GM12878_IgG_Pol2_sequence_rep7_laneB_FC20698AA_031908_s_6.fastq >> wgEncodeYaleChIPseqRawDataRep7Gm12878Pol2Musigg.fastq
/bin/gzip wgEncodeYaleChIPseqRawDataRep7Gm12878Pol2Musigg.fastq
mv wgEncodeYaleChIPseqRawDataRep7Gm12878Pol2Musigg.fastq.gz /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/
# Fixed that but now I am suspicious!
ll | sort -n -k 5 > tmp.txt
uniq --skip-fields=4 -w 7 --all-repeated=separate tmp.txt > tmp2.txt
# This works with fastq, tagAligns and some bedGraphs. Not peaks...
grep Peak tmp.txt | uniq --skip-fields=4 -w 9 --all-repeated=separate | h
-rw-rw-r-- 1 qateam protein 926529 Jan 5 18:47 wgEncodeYaleChIPseqPeaksHelas3Baf155.narrowPeak.gz
-rw-rw-r-- 1 qateam protein 926529 Jan 12 23:05 wgEncodeYaleChIPseqPeaksHelas3Baf155Musigg.narrowPeak.gz
-rw-rw-r-- 1 qateam protein 125883138 Jan 5 18:53 wgEncodeYaleChIPseqSignalGm12891Mouseigg.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 125883138 Jan 12 23:18 wgEncodeYaleChIPseqSignalGm12891MusiggMusigg.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 133051817 Jan 5 11:14 wgEncodeYaleChIPseqSignalGm10847Input.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 133051821 Jan 12 21:01 wgEncodeYaleChIPseqSignalGm10847MusiggMusigg.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 137235542 Jan 5 18:49 wgEncodeYaleChIPseqAlignmentsRep1Gm12891Mouseigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 137235542 Jan 12 23:11 wgEncodeYaleChIPseqAlignmentsRep1Gm12891MusiggMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 142489318 Jan 5 18:54 wgEncodeYaleChIPseqAlignmentsRep2Gm12891Mouseigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 142489318 Jan 12 23:10 wgEncodeYaleChIPseqAlignmentsRep2Gm12891MusiggMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 145708360 Jan 5 11:09 wgEncodeYaleChIPseqAlignmentsRep1Gm10847Input.tagAlign.gz
-rw-rw-r-- 1 qateam protein 145708364 Jan 12 21:02 wgEncodeYaleChIPseqAlignmentsRep1Gm10847MusiggMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 147122984 Jan 5 11:07 wgEncodeYaleChIPseqAlignmentsRep2Gm10847Input.tagAlign.gz
-rw-rw-r-- 1 qateam protein 147122988 Jan 12 20:55 wgEncodeYaleChIPseqAlignmentsRep2Gm10847MusiggMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 189491929 Jan 12 16:49 wgEncodeYaleChIPseqAlignmentsRep4Gm12878NfkbMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 189496685 Jan 13 17:20 wgEncodeYaleChIPseqAlignmentsRep1Gm18505Pol2Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 207201999 Jan 5 18:29 wgEncodeYaleChIPseqAlignmentsRep2Helas3Baf155.tagAlign.gz
-rw-rw-r-- 1 qateam protein 207201999 Jan 12 22:55 wgEncodeYaleChIPseqAlignmentsRep2Helas3Baf155Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 217684278 Jan 5 18:47 wgEncodeYaleChIPseqAlignmentsRep1Helas3Baf155.tagAlign.gz
-rw-rw-r-- 1 qateam protein 217684278 Jan 12 23:01 wgEncodeYaleChIPseqAlignmentsRep1Helas3Baf155Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 226757984 Jan 5 11:10 wgEncodeYaleChIPseqRawDataRep1Gm10847Input.fastq.gz
-rw-rw-r-- 1 qateam protein 226757988 Jan 12 20:56 wgEncodeYaleChIPseqRawDataRep1Gm10847MusiggMusigg.fastq.gz
-rw-rw-r-- 1 qateam protein 229908100 Jan 5 11:06 wgEncodeYaleChIPseqRawDataRep2Gm10847Input.fastq.gz
-rw-rw-r-- 1 qateam protein 229908104 Jan 12 21:04 wgEncodeYaleChIPseqRawDataRep2Gm10847MusiggMusigg.fastq.gz
-rw-rw-r-- 1 qateam protein 245108337 Jan 5 18:45 wgEncodeYaleChIPseqAlignmentsRep3Helas3Baf155.tagAlign.gz
-rw-rw-r-- 1 qateam protein 245108337 Jan 12 22:43 wgEncodeYaleChIPseqAlignmentsRep3Helas3Baf155Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 277154901 Jan 12 16:50 wgEncodeYaleChIPseqAlignmentsRep1K562Brg1Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 277154903 Jan 12 18:29 wgEncodeYaleChIPseqAlignmentsRep1Helas3Brg1Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 320435111 Jan 5 20:13 wgEncodeYaleChIPseqSignalK562Mouseigg.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 320435111 Jan 12 22:05 wgEncodeYaleChIPseqSignalK562MusiggMusigg.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 337083295 Jan 5 18:39 wgEncodeYaleChIPseqSignalHelas3Baf155.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 337083295 Jan 12 22:53 wgEncodeYaleChIPseqSignalHelas3Baf155Musigg.bedGraph4.gz
-rw-rw-r-- 1 qateam protein 340449586 Jan 5 19:55 wgEncodeYaleChIPseqAlignmentsRep2K562Mouseigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 340449590 Jan 12 22:06 wgEncodeYaleChIPseqAlignmentsRep2K562MusiggMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 340515577 Jan 5 20:13 wgEncodeYaleChIPseqAlignmentsRep1K562Mouseigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 340515581 Jan 12 21:41 wgEncodeYaleChIPseqAlignmentsRep1K562MusiggMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 345738258 Jan 12 16:58 wgEncodeYaleChIPseqAlignmentsRep2K562Brg1Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 345738260 Jan 12 18:26 wgEncodeYaleChIPseqAlignmentsRep2Helas3Brg1Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 423373151 Jan 5 18:58 wgEncodeYaleChIPseqRawDataRep2Gm12891Mouseigg.fastq.gz
-rw-rw-r-- 1 qateam protein 423373151 Jan 12 23:14 wgEncodeYaleChIPseqRawDataRep2Gm12891MusiggMusigg.fastq.gz
-rw-rw-r-- 1 qateam protein 424432011 Jan 5 19:01 wgEncodeYaleChIPseqRawDataRep1Gm12891Mouseigg.fastq.gz
-rw-rw-r-- 1 qateam protein 424432011 Jan 12 23:08 wgEncodeYaleChIPseqRawDataRep1Gm12891MusiggMusigg.fastq.gz
-rw-rw-r-- 1 qateam protein 445134984 Jan 12 16:54 wgEncodeYaleChIPseqRawDataRep1K562Brg1Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 445134986 Jan 12 18:21 wgEncodeYaleChIPseqRawDataRep1Helas3Brg1Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 480704394 Jan 5 18:22 wgEncodeYaleChIPseqRawDataRep2Helas3Baf155.fastq.gz
-rw-rw-r-- 1 qateam protein 480704394 Jan 12 22:41 wgEncodeYaleChIPseqRawDataRep2Helas3Baf155Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 495842330 Jan 5 18:42 wgEncodeYaleChIPseqRawDataRep1Helas3Baf155.fastq.gz
-rw-rw-r-- 1 qateam protein 495842330 Jan 12 22:59 wgEncodeYaleChIPseqRawDataRep1Helas3Baf155Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 509759928 Jan 5 19:59 wgEncodeYaleChIPseqRawDataRep1K562Mouseigg.fastq.gz
-rw-rw-r-- 1 qateam protein 509759932 Jan 12 21:51 wgEncodeYaleChIPseqRawDataRep1K562MusiggMusigg.fastq.gz
-rw-rw-r-- 1 qateam protein 512145606 Jan 12 17:13 wgEncodeYaleChIPseqRawDataRep2K562Brg1Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 512145608 Jan 12 18:42 wgEncodeYaleChIPseqRawDataRep2Helas3Brg1Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 548636590 Jan 5 20:17 wgEncodeYaleChIPseqRawDataRep2K562Mouseigg.fastq.gz
-rw-rw-r-- 1 qateam protein 548636594 Jan 12 21:45 wgEncodeYaleChIPseqRawDataRep2K562MusiggMusigg.fastq.gz
-rw-rw-r-- 1 qateam protein 564079048 Jan 5 18:27 wgEncodeYaleChIPseqRawDataRep3Helas3Baf155.fastq.gz
-rw-rw-r-- 1 qateam protein 564079048 Jan 12 23:05 wgEncodeYaleChIPseqRawDataRep3Helas3Baf155Musigg.fastq.gz
========= Fix:
rm wgEncodeYaleChIPseqPeaksHelas3Baf155.narrowPeak.gz
rm wgEncodeYaleChIPseqSignalGm12891Mouseigg.bedGraph4.gz
rm wgEncodeYaleChIPseqSignalGm10847Input.bedGraph4.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Gm12891Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm12891Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Gm10847Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Gm10847Input.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep2Helas3Baf155.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1Helas3Baf155.tagAlign.gz
rm wgEncodeYaleChIPseqRawDataRep1Gm10847Input.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep2Gm10847Input.fastq.gz
rm wgEncodeYaleChIPseqAlignmentsRep3Helas3Baf155.tagAlign.gz
rm wgEncodeYaleChIPseqSignalK562Mouseigg.bedGraph4.gz
rm wgEncodeYaleChIPseqSignalHelas3Baf155.bedGraph4.gz
rm wgEncodeYaleChIPseqAlignmentsRep2K562Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqAlignmentsRep1K562Mouseigg.tagAlign.gz
rm wgEncodeYaleChIPseqRawDataRep2Gm12891Mouseigg.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep1Gm12891Mouseigg.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep2Helas3Baf155.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep1Helas3Baf155.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep1K562Mouseigg.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep2K562Mouseigg.fastq.gz
rm wgEncodeYaleChIPseqRawDataRep3Helas3Baf155.fastq.gz
-rw-rw-r-- 1 qateam protein 189491929 Jan 12 16:49 wgEncodeYaleChIPseqAlignmentsRep4Gm12878NfkbMusigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 189496685 Jan 13 17:20 wgEncodeYaleChIPseqAlignmentsRep1Gm18505Pol2Musigg.tagAlign.gz
zdiff wgEncodeYaleChIPseqAlignmentsRep4Gm12878NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm18505Pol2Musigg.tagAlign.gz | h
>> Lots of diffs
-rw-rw-r-- 1 qateam protein 277154901 Jan 12 16:50 wgEncodeYaleChIPseqAlignmentsRep1K562Brg1Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 277154903 Jan 12 18:29 wgEncodeYaleChIPseqAlignmentsRep1Helas3Brg1Musigg.tagAlign.gz
zdiff wgEncodeYaleChIPseqAlignmentsRep1K562Brg1Musigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Helas3Brg1Musigg.tagAlign.gz | h
>> EYE-dentical
-rw-rw-r-- 1 qateam protein 345738258 Jan 12 16:58 wgEncodeYaleChIPseqAlignmentsRep2K562Brg1Musigg.tagAlign.gz
-rw-rw-r-- 1 qateam protein 345738260 Jan 12 18:26 wgEncodeYaleChIPseqAlignmentsRep2Helas3Brg1Musigg.tagAlign.gz
zdiff wgEncodeYaleChIPseqAlignmentsRep2K562Brg1Musigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Helas3Brg1Musigg.tagAlign.gz | h
>> EYE-dentical
-rw-rw-r-- 1 qateam protein 445134984 Jan 12 16:54 wgEncodeYaleChIPseqRawDataRep1K562Brg1Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 445134986 Jan 12 18:21 wgEncodeYaleChIPseqRawDataRep1Helas3Brg1Musigg.fastq.gz
zdiff wgEncodeYaleChIPseqRawDataRep1K562Brg1Musigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Helas3Brg1Musigg.fastq.gz | h
>> EYE-dentical
-rw-rw-r-- 1 qateam protein 512145606 Jan 12 17:13 wgEncodeYaleChIPseqRawDataRep2K562Brg1Musigg.fastq.gz
-rw-rw-r-- 1 qateam protein 512145608 Jan 12 18:42 wgEncodeYaleChIPseqRawDataRep2Helas3Brg1Musigg.fastq.gz
zdiff wgEncodeYaleChIPseqRawDataRep2K562Brg1Musigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Helas3Brg1Musigg.fastq.gz | h
>> EYE-dentical
### There is a real problem here!
../893/data
K562_IgG_Brg1.wig
K562_IgG_Brg1_narrowPeak.bed
K562_IgG_Brg1_sequence_rep1_laneA_FC30AKR_20080917_s_1.fastq
K562_IgG_Brg1_sequence_rep1_laneB_FC30AKT_20080924_s_2.fastq
K562_IgG_Brg1_sequence_rep1_laneC_FC30V3HHM_20090120_s_7.fastq
K562_IgG_Brg1_sequence_rep2_laneA_FC30AKR_20080917_s_2.fastq
K562_IgG_Brg1_sequence_rep2_laneB_FC30AKT_20080924_s_3.fastq
K562_IgG_Brg1_sequence_rep2_laneC_FC30B3N_20080928_s_6.fastq
K562_IgG_Brg1_sequence_rep2_laneD_FC30V1JHM_20090121_s_2.fastq
K562_IgG_Brg1_tagAlign_rep1_laneA_FC30AKR_20080917_s_1.bed
K562_IgG_Brg1_tagAlign_rep1_laneB_FC30AKT_20080924_s_2.bed
K562_IgG_Brg1_tagAlign_rep1_laneC_FC30V3HHM_20090120_s_7.bed
K562_IgG_Brg1_tagAlign_rep2_laneA_FC30AKR_20080917_s_2.bed
K562_IgG_Brg1_tagAlign_rep2_laneB_FC30AKT_20080924_s_3.bed
K562_IgG_Brg1_tagAlign_rep2_laneC_FC30B3N_20080928_s_6.bed
K562_IgG_Brg1_tagAlign_rep2_laneD_FC30V1JHM_20090121_s_2.bed
[hgwdev:tdreszer 891> ls ../891/data
HeLa-S3_IgG_Brg1.wig
HeLa-S3_IgG_Brg1_narrowPeak.bed
HeLa-S3_IgG_Brg1_sequence_rep1_laneA_FC30AKR_20080917_s_1.fastq
HeLa-S3_IgG_Brg1_sequence_rep1_laneB_FC30AKT_20080924_s_2.fastq
HeLa-S3_IgG_Brg1_sequence_rep1_laneC_FC30V3HHM_20090120_s_7.fastq
HeLa-S3_IgG_Brg1_sequence_rep2_laneA_FC30AKR_20080917_s_2.fastq
HeLa-S3_IgG_Brg1_sequence_rep2_laneB_FC30AKT_20080924_s_3.fastq
HeLa-S3_IgG_Brg1_sequence_rep2_laneC_FC30B3N_20080928_s_6.fastq
HeLa-S3_IgG_Brg1_sequence_rep2_laneD_FC30V1JHM_20090121_s_2.fastq
HeLa-S3_IgG_Brg1_tagAlign_rep1_laneA_FC30AKR_20080917_s_1.bed
HeLa-S3_IgG_Brg1_tagAlign_rep1_laneB_FC30AKT_20080924_s_2.bed
HeLa-S3_IgG_Brg1_tagAlign_rep1_laneC_FC30V3HHM_20090120_s_7.bed
HeLa-S3_IgG_Brg1_tagAlign_rep2_laneA_FC30AKR_20080917_s_2.bed
HeLa-S3_IgG_Brg1_tagAlign_rep2_laneB_FC30AKT_20080924_s_3.bed
HeLa-S3_IgG_Brg1_tagAlign_rep2_laneC_FC30B3N_20080928_s_6.bed
HeLa-S3_IgG_Brg1_tagAlign_rep2_laneD_FC30V1JHM_20090121_s_2.bed
### Helas3Brg1Musigg is revoked!
mv *Helas3Brg1Musigg* revokedJan2010/
/cluster/data/encode/pipeline/bin/encodeStatus.pl 633 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 634 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 669 approved
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### Officailly revoked
update projects set status = "revoked" where id in (891,950,995,1085);
| 891 | YDH_HeLa-S3_IgG_Brg1 | revoked | 6 | 2010-01-05 12:56:06 |
| 950 | YDH_HUVEC_Pol2 | revoked | 6 | 2010-01-08 22:51:27 |
| 995 | YDH_HUVEC_Jun | revoked | 6 | 2010-01-11 17:20:20 |
| 1085 | YDH_HUVEC_Max | revoked | 6 | 2010-01-15 16:38:48 |
### NOTE: Have tables/files for HUVEC and will revert to displayed/approved when input is available.
### NOTE: When Yale can resubmit HeLa-S3/Brg1/IgG-mus, then change from revoked -> loaded and then unload!
2010-03-05 Loading newly submitted rabit IgGs through the back door
===================================================================
make submission named "YDH_GM10847_Rabbit_IgG"
cd {pip}
mkdir 1108
cd 1108
mv ../../ftp/prod/pcayting/GM10847_Rabbit_IgG.tgz .
mv GM10847_Rabbit_IgG.tgz 001_YDH_GM10847_Rabbit_IgG.tgz
tar -xzf 001_YDH_GM10847_Rabbit_IgG.tgz &
edit DAF and DDF
1) add input column to DDF and replace Rabbit_IgG with "IgG-rab"
2) fill treatment column with "None"
3) Fill anitbody column with "Input"
4) Change DAF to add treatment, inptut to variables and quicken validation
5) tagAligns, fastq has replicates
6) Removed RawSignal from the DAF
update projects set status = "uploaded" where id = 1108;
# Success, so carry on with other IgG-rabs:
mkdir 1109
mkdir 1110
mkdir 1111
mkdir 1112
mkdir 1113
mkdir 1114
mkdir 1115
mkdir 1116
mkdir 1117
mv ../ftp/prod/pcayting/GM12878_Rabbit_IgG.tgz 1109/001_GM12878_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM12891_Rabbit_IgG.tgz 1111/001_GM12891_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM12892_Rabbit_IgG.tgz 1110/001_GM12892_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM15510_Rabbit_IgG.tgz 1112/001_GM15510_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM18505_Rabbit_IgG.tgz 1113/001_GM18505_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM18526_Rabbit_IgG.tgz 1114/001_GM18526_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM18951_Rabbit_IgG.tgz 1115/001_GM18951_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM19099_Rabbit_IgG.tgz 1116/001_GM19099_Rabbit_IgG.tgz
mv ../ftp/prod/pcayting/GM19193_Rabbit_IgG.tgz 1117/001_GM19193_Rabbit_IgG.tgz
cd 1109
tar -xzf *.tgz &
# stack up only 3 at at time
update projects set status = "uploaded" where id >= 1109;
# "validate" through the pipeline
cd {downloadsDir}
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1108/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1109/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1110/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1111/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1112/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1113/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1114/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1115/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1116/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1117/out/fileDb.ra | grep parentTable >> tmp.txt
e tmp.txt
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1108 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1109 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1110 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1111 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1112 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1113 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1114 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1115 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1116 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1117 displayed
# 3 more
mkdir 1118
mkdir 1119
mkdir 1120
mv ../ftp/prod/pcayting/HUVEC_IgG_Control.tgz 1118/001_HUVEC_IgG_Control.tgz
mv ../ftp/prod/pcayting/HeLa_Brg1.tgz 1118/001_HeLa_Brg1.tgz
mv ../ftp/prod/pcayting/HeLa_IgG_Control.tgz 1118/001_HeLa_IgG_Control.tgz
cd 1118,1119,1120
tar -xzf *.tgz &
update projects set status = "uploaded" where id = 1118;
update projects set status = "uploaded" where id = 1119;
### Must edit fileDb.ra to reposition all those GM* which should point to IgG-rab instead of IgG-mus.
Done.
### Would be good to change the following names
rename table wgEncodeYaleChIPseqPeaksGm10847NfkbMusigg to wgEncodeYaleChIPseqPeaksGm10847NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm12878NfkbMusigg to wgEncodeYaleChIPseqPeaksGm12878NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm12891NfkbMusigg to wgEncodeYaleChIPseqPeaksGm12891NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm12892NfkbMusigg to wgEncodeYaleChIPseqPeaksGm12892NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm15510NfkbMusigg to wgEncodeYaleChIPseqPeaksGm15510NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm18505NfkbMusigg to wgEncodeYaleChIPseqPeaksGm18505NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm18526NfkbMusigg to wgEncodeYaleChIPseqPeaksGm18526NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm18951NfkbMusigg to wgEncodeYaleChIPseqPeaksGm18951NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm19099NfkbMusigg to wgEncodeYaleChIPseqPeaksGm19099NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm19193NfkbMusigg to wgEncodeYaleChIPseqPeaksGm19193NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm10847NfkbMusigg to wgEncodeYaleChIPseqSignalGm10847NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm12878NfkbMusigg to wgEncodeYaleChIPseqSignalGm12878NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm12891NfkbMusigg to wgEncodeYaleChIPseqSignalGm12891NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm12892NfkbMusigg to wgEncodeYaleChIPseqSignalGm12892NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm15510NfkbMusigg to wgEncodeYaleChIPseqSignalGm15510NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm18505NfkbMusigg to wgEncodeYaleChIPseqSignalGm18505NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm18526NfkbMusigg to wgEncodeYaleChIPseqSignalGm18526NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm18951NfkbMusigg to wgEncodeYaleChIPseqSignalGm18951NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm19099NfkbMusigg to wgEncodeYaleChIPseqSignalGm19099NfkbIggrab;
rename table wgEncodeYaleChIPseqSignalGm19193NfkbMusigg to wgEncodeYaleChIPseqSignalGm19193NfkbIggrab;
rename table wgEncodeYaleChIPseqPeaksGm12878Rad21 to wgEncodeYaleChIPseqPeaksGm12878Rad21Iggrab;
rename table wgEncodeYaleChIPseqSignalGm12878Rad21 to wgEncodeYaleChIPseqSignalGm12878Rad21Iggrab;
mv wgEncodeYaleChIPseqAlignmentsRep1Gm10847NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm10847NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm12878NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm12891NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12891NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm12892NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12892NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm15510NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm15510NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm18505NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm18505NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm18526NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm18526NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm18951NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm18951NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm19099NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm19099NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm19193NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm19193NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm10847NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm10847NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm12878NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm12891NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12891NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm12892NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12892NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm15510NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm15510NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm18505NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm18505NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm18526NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm18526NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm18951NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm18951NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm19099NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm19099NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm19193NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm19193NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm10847NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm10847NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm12878NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm12878NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm12891NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm12891NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm12892NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm12892NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm15510NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm15510NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm18505NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm18505NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm18526NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm18526NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm18951NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm18951NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm19099NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm19099NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep3Gm19193NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm19193NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep4Gm10847NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep4Gm10847NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep4Gm12878NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep4Gm12878NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep4Gm15510NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep4Gm15510NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep4Gm18505NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep4Gm18505NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep4Gm18951NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep4Gm18951NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep5Gm10847NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep5Gm10847NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep5Gm15510NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep5Gm15510NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep5Gm18505NfkbMusigg.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep5Gm18505NfkbIggrab.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksGm10847NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm10847NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm12878NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm12891NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12891NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm12892NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12892NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm15510NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm15510NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm18505NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm18505NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm18526NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm18526NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm18951NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm18951NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm19099NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm19099NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqPeaksGm19193NfkbMusigg.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm19193NfkbIggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm10847NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm10847NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm12878NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm12891NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12891NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm12892NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12892NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm15510NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm15510NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm18505NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm18505NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm18526NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm18526NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm18951NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm18951NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm19099NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm19099NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm19193NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm19193NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm10847NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm10847NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm12878NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm12891NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12891NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm12892NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12892NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm15510NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm15510NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm18505NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm18505NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm18526NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm18526NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm18951NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm18951NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm19099NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm19099NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm19193NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm19193NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm10847NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm10847NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm12878NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm12878NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm12891NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm12891NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm12892NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm12892NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm15510NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm15510NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm18505NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm18505NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm18526NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm18526NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm18951NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm18951NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm19099NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm19099NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep3Gm19193NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm19193NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep4Gm10847NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep4Gm10847NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep4Gm12878NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep4Gm12878NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep4Gm15510NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep4Gm15510NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep4Gm18505NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep4Gm18505NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep4Gm18951NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep4Gm18951NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep5Gm10847NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep5Gm10847NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep5Gm15510NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep5Gm15510NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep5Gm18505NfkbMusigg.fastq.gz wgEncodeYaleChIPseqRawDataRep5Gm18505NfkbIggrab.fastq.gz
mv wgEncodeYaleChIPseqSignalGm10847NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm10847NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm12878NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm12891NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12891NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm12892NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12892NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm15510NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm15510NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm18505NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm18505NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm18526NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm18526NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm18951NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm18951NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm19099NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm19099NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqSignalGm19193NfkbMusigg.bedGraph4.gz wgEncodeYaleChIPseqSignalGm19193NfkbIggrab.bedGraph4.gz
mv wgEncodeYaleChIPseqAlignmentsRep1Gm12878Rad21.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878Rad21Iggrab.tagAlign.gz
mv wgEncodeYaleChIPseqAlignmentsRep2Gm12878Rad21.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878Rad21Iggrab.tagAlign.gz
mv wgEncodeYaleChIPseqPeaksGm12878Rad21.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Rad21Iggrab.narrowPeak.gz
mv wgEncodeYaleChIPseqRawDataRep1Gm12878Rad21.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878Rad21Iggrab.fastq.gz
mv wgEncodeYaleChIPseqRawDataRep2Gm12878Rad21.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878Rad21Iggrab.fastq.gz
mv wgEncodeYaleChIPseqSignalGm12878Rad21.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878Rad21Iggrab.bedGraph4.gz
Done.
# edit trackDb.wgEncode.ra and fileDb.ra for name changes
make alpha DBS=hg18
encodeDownloadsPage.pl index.html .
# take care of these:
hg18.wgEncodeYaleChIPseqSignalGm10847InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm10847InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12891InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12892InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm15510InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18505InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18526InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm18951InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19099InputIggrab has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm19193InputIggrab has 1 records with end > chromSize.
update wgEncodeYaleChIPseqSignalGm10847InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm12878InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm12891InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm12892InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm15510InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18505InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18526InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm18951InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19099InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalGm19193InputIggrab y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
### These 3 have some questions on them so I will not load them yet.
1) Huvec input is probably std. confirm? YES
2) HeLa/Brg1 is probably paired with IgG-mus YES
3) HeLa/IgG is a mystery input... What should it be?
# dropped 1120
# unrevoke HUVEC
cd {downloadsDir}
mv revkedJan2010/*Huvec* .
e fileDb.ra to dataVersion="post ENCODE Jan 2010 Freeze" and add 1118 submission Huvec input=std
e trackDb.wgEncode.ra to uncomment out Huvecs, add "post" to dataVersion and add 1118 submission Huvec input=std
make alpha DBS=hg18
encodeDownloadsPage.pl index.html .
e fileDb.ra to add 1119
e trackDb.wgEncode.ra to add 1119
make alpha DBS=hg18
encodeDownloadsPage.pl index.html .
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1118 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1119 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 950 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 995 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 1085 displayed
update projects set user_id = 39 where id in (1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1118,1119);
### Need approval for these:
| 950 | YDH_HUVEC_Pol2 | displayed | 39 |
| 995 | YDH_HUVEC_Jun | displayed | 39 |
| 1085 | YDH_HUVEC_Max | displayed | 39 |
| 1108 | YDH_GM10847_Rabbit_IgG | displayed | 39 |
| 1109 | YDH_GM12878_Rabbit_IgG | displayed | 39 |
| 1110 | YDH_GM12892_Rabbit_IgG | displayed | 39 |
| 1111 | YDH_GM12891_Rabbit_IgG | displayed | 39 |
| 1112 | YDH_GM15510_Rabbit_IgG | displayed | 39 |
| 1113 | YDH_GM18505_Rabbit_IgG | displayed | 39 |
| 1114 | YDH_GM18526_Rabbit_IgG | displayed | 39 |
| 1115 | YDH_GM18951_Rabbit_IgG | displayed | 39 |
| 1116 | YDH_GM19099_Rabbit_IgG | displayed | 39 |
| 1117 | YDH_GM19193_Rabbit_IgG | displayed | 39 |
| 1118 | YDH_HUVEC_IgG_Control | displayed | 39 |
| 1119 | YDH_HeLa_Brg1 | displayed | 39 |
wgEncodeYaleChIPseqSignalHuvecInputStd
wgEncodeYaleChIPseqSignalHelas3Brg1Iggmus
wgEncodeYaleChIPseqPeaksHelas3Brg1Iggmus
update wgEncodeYaleChIPseqSignalHuvecInputStd y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalHelas3Brg1Iggmus y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
2010-03-25 Getting release3 ready
===============================
Seem to have lost 2 tables but not the files (subId=1046):
wgEncodeYaleChIPseqPeaksGm19099Pol2Musigg
wgEncodeYaleChIPseqSignalGm19099Pol2Musigg
cd {downloadsDir}
mkdir save
mv wgEncodeYaleChIPseqPeaksGm19099Pol*.* save
mv wgEncodeYaleChIPseqSignalGm19099Pol*.* save
cd {pip}/1046
e out/load.ra # remove all but peak and Signal
~qateam/bin/scripts/doEncodeLoad.pl . /hive/groups/encode/dcc/pipeline/encpipeline_prod/1046
# Confirm the tables are there. Confirm the files are the same. mv save/*.gz back to downloadsDir
# confirm in browser.
Add pushQ entry and put it in A at the end of the ENCODE list
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1108 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1109 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1110 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1111 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1112 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1113 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1114 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1115 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1116 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1117 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1118 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1119 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 633 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 634 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 669 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 739 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 757 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 787 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 853 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 860 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 861 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 862 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 863 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 864 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 865 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 888 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 890 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 892 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 893 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 894 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 895 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 900 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 928 reviewing
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 950 approved
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### Rerunning encodeDownloadsPage with -checksum so be sure to copy md5sum.txt again
2010-04-12 Release 3 in pushQ
=============================
update wgEncodeYaleChIPseqSignalHelas3JundRabigg y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562Stat1Ifng6h y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeYaleChIPseqSignalK562bSetdb1Mnase y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
2010-04-12 Loadeing metaTbl for hg18
====================================
cd {tdb}
grep metadata trackdDb.wgencode.ra | grep Snyder > testing/metaYaleTfbs.txt
cd testing
# edit remove the dups
metaTblUpdate -db=hg18 metaYaleTfbs.txt
Using table named 'hg18.metaTbl_tdreszer'.
Read 301 metadata objects from metaYaleTfbs.txt
Affected 5006 row(s) in hg18.metaTbl_tdreszer
cd {downloads}
metaTblUpdate -db=hg18 fileDb.ra
Read 861 metadata objects from fileDb.ra
Affected 14951 row(s) in hg18.metaTbl_tdreszer
encodeDownloadsPage.pl -metaTbl=metaTbl_tdreszer meta.html .
encodeDownloadsPage.pl -noMetaTbl noMeta.html .
wl meta.html
1112 meta.html
wl noMeta.html
1112 noMeta.html
diff meta.html noMeta.html
# identical!
cd {tdb}/testing
metaTblPrint -db=hg18 -vars="grant=Snyder" -ra > metaYaleTfbs.ra
Using table named 'hg18.metaTbl_tdreszer'.
objects:1160 vars:19957
# Expected 1073 Difference? Must be versioned tables and files which were in fileDb.ra but are no longer in the downloads dir.
# Clean extra entries?
After doing some greps and diffs I have a list of 87 that are not the downloads dir
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep1Gm10847Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep1Gm12891Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep1Helas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep1Helas3Brg1Musigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep1K562Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep2Gm10847Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep2Gm12891Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep2Helas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep2Helas3Brg1Musigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep2K562Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqAlignmentsRep3Helas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep1Gm10847Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep1Gm12891Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep1Helas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep1Helas3Brg1Musigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep1K562Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep1K562Pol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep2Gm10847Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep2Gm12891Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep2Helas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep2Helas3Brg1Musigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep2K562Mouseigg
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep2K562Pol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawDataRep3Helas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalHepg2bInput
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalK562Ifna30Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalK562Ifna6hInput
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalK562Ifng30Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalK562Ifng6hInput
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalK562bInput
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalNt2d1Input
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1Hct116Pol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1Hepg2bTr4
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Bdp1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Brf1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna30Cmyc
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna30Pol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna30Stat1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna30Stat2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna6hCjun
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna6hCmyc
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna6hPol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna6hStat1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifna6hStat2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifng30Cjun
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifng6hCjun
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifng6hCmyc
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Ifng6hPol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Rpc155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562Sirt6
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562bE2f4
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562bE2f6
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562bSetdb1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1K562bTr4
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1Nt2d1Suz12
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep1Nt2d1Yy1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2Hct116Pol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2Hepg2bTr4
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Bdp1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Brf1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna30Cmyc
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna30Pol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna30Stat1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna30Stat2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna6hCjun
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna6hCmyc
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna6hPol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna6hStat1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifna6hStat2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifng30Cjun
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifng6hCjun
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifng6hCmyc
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Ifng6hPol2
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Rpc155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562Sirt6
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562bE2f4
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562bE2f6
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562bSetdb1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2K562bTr4
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2Nt2d1Suz12
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep2Nt2d1Yy1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep3K562Bdp1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRawSignalRep3K562Brf1
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRel2RawSignalRep1Helas3Largefragment
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqRel2RawSignalRep2Helas3Largefragment
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqSignalHelas3Baf155
metaTblUpdate -db=hg18 -delete -obj=wgEncodeYaleChIPseqSignalK562Mouseigg
encodeDownloadsPage.pl -metaTbl=metaTbl_tdreszer meta.html .
encodeDownloadsPage.pl -noMetaTbl noMeta.html .
diff meta.html noMeta.html
# identical!
cd {tdb}/testing
metaTblPrint -db=hg18 -vars="grant=Snyder" -ra > metaYaleTfbs.ra
Using table named 'hg18.metaTbl_tdreszer'.
objects:1073 vars:18389
metaTblUpdate -db=hg18 -table=metaTbl metaYaleTfbs.ra
Read 1073 metadata objects from metaYaleTfbs.ra
Affected 18389 row(s) in hg18.metaTbl
/cluster/data/encode/pipeline/bin/encodeStatus.pl 331 displayed
2010-04-20 Fix 'input' once and for all ??
==========================================
select distinct var,val from mdb_tdreszer where obj like "wgEncodeYaleChIP%" and var in ("cell","treatment","antibody","protocol","input");
95 rows in set (0.06 sec) ## No protocol
select distinct t1.val,t2.val,t3.val,t4.val from mdb_tdreszer t1,mdb_tdreszer t2,mdb_tdreszer t3,mdb_tdreszer t4 where t1.obj like "wgEncodeYaleChIP%"
and t1.obj = t2.obj and t2.obj = t3.obj and t3.obj = t4.obj
and t1.var = "cell" and t2.var = "treatment" and t3.var = "antibody" and t4.var = "input"
order by t1.val,t2.val,t3.val,t4.val;
50 rows in set (0.08 sec) ### Missing values!
select count(*) from mdb_tdreszer where obj like "wgEncodeYaleChIP%" and var = "cell"; 1073, "antibody" 1073, "input" 1073, "treatment" 271
# Plan: print current mdb, update all objs to have default treatment=None, THEN reupdate with current settings in file
mdbPrint hg18 -vars="composite=wgEncodeYaleChIPseq" -ra > mdbYale.ra
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq" -var=treatment -val=None -test
mdbUpdate hg18 mdbYale.ra
select distinct t1.val cell,t2.val treatment,t3.val antibody,t4.val input from mdb_tdreszer t1,mdb_tdreszer t2,mdb_tdreszer t3,mdb_tdreszer t4 where t1.obj like "wgEncodeYaleChIP%"
and t1.obj = t2.obj and t2.obj = t3.obj and t3.obj = t4.obj
and t1.var = "cell" and t2.var = "treatment" and t3.var = "antibody" and t4.var = "input"
order by t1.val,t2.val,t3.val,t4.val;
+-----------+-------------+------------+----------------+
| cell | treatment | antibody | input |
+-----------+-------------+------------+----------------+
| GM10847 | None | Input | IgG-mus |
| GM10847 | None | Input | IgG-rab |
| GM10847 | None | NFKB | IgG-rab |
| GM10847 | None | Pol2 | IgG-mus |
| GM12878 | None | Input | IgG-mus |
| GM12878 | None | Input | IgG-rab |
| GM12878 | None | Input | std |
| GM12878 | None | JunD | std |
| GM12878 | None | Max | std |
| GM12878 | None | NFKB | IgG-rab |
| GM12878 | None | Pol2 | IgG-mus |
| GM12878 | None | Pol2 | std |
| GM12878 | None | Pol3 | std |
| GM12878 | None | Rad21 | IgG-rab |
| GM12878 | None | TR4 | std |
| GM12878 | None | YY1 | std |
| GM12878 | None | ZZZ3 | std |
| GM12878 | None | c-Fos | std |
| GM12878 | TNFa | NFKB | std |
| GM12891 | None | Input | IgG-mus |
| GM12891 | None | Input | IgG-rab |
| GM12891 | None | NFKB | IgG-rab |
| GM12891 | None | Pol2 | IgG-mus |
| GM12892 | None | Input | IgG-mus |
| GM12892 | None | Input | IgG-rab |
| GM12892 | None | NFKB | IgG-rab |
| GM12892 | None | Pol2 | IgG-mus |
| GM15510 | None | Input | IgG-mus |
| GM15510 | None | Input | IgG-rab |
| GM15510 | None | NFKB | IgG-rab |
| GM15510 | None | Pol2 | IgG-mus |
| GM18505 | None | Input | IgG-mus |
| GM18505 | None | Input | IgG-rab |
| GM18505 | None | NFKB | IgG-rab |
| GM18505 | None | Pol2 | IgG-mus |
| GM18526 | None | Input | IgG-mus |
| GM18526 | None | Input | IgG-rab |
| GM18526 | None | NFKB | IgG-mrabus |
| GM18526 | None | NFKB | IgG-rab |
| GM18526 | None | Pol2 | IgG-mus |
| GM18951 | None | Input | IgG-mus |
| GM18951 | None | Input | IgG-rab |
| GM18951 | None | NFKB | IgG-rab |
| GM18951 | None | Pol2 | IgG-mus |
| GM19099 | None | Input | IgG-mus |
| GM19099 | None | Input | IgG-rab |
| GM19099 | None | NFKB | IgG-rab |
| GM19099 | None | Pol2 | IgG-mus |
| GM19193 | None | Input | IgG-mus |
| GM19193 | None | Input | IgG-rab |
| GM19193 | None | NFKB | IgG-rab |
| GM19193 | None | Pol2 | IgG-mus |
| HCT-116 | None | Input | UCDavis |
| HCT-116 | None | Pol2 | UCDavis |
| HCT-116 | None | TCF4 | UCDavis |
| HCT-116 | None | TCF7L2 | UCDavis |
| HEK293(b) | None | Input | std |
| HEK293(b) | None | Pol2 | std |
| HUVEC | None | Input | std |
| HUVEC | None | Max | std |
| HUVEC | None | Pol2 | std |
| HUVEC | None | c-Jun | std |
| HeLa-S3 | IFNg | STAT1 | std |
| HeLa-S3 | IFNg30 | Input | std |
| HeLa-S3 | IFNg30 | STAT1 | std |
| HeLa-S3 | None | AP-2alpha | std |
| HeLa-S3 | None | AP-2gamma | std |
| HeLa-S3 | None | BAF155 | IgG-mus |
| HeLa-S3 | None | BAF170 | IgG-mus |
| HeLa-S3 | None | BDP1 | std |
| HeLa-S3 | None | BRF1 | std |
| HeLa-S3 | None | BRF2 | std |
| HeLa-S3 | None | Brg1 | IgG-mus |
| HeLa-S3 | None | E2F1 | std |
| HeLa-S3 | None | E2F4 | std |
| HeLa-S3 | None | E2F6 | std |
| HeLa-S3 | None | HA-E2F1 | std |
| HeLa-S3 | None | HA-F2F1 | std |
| HeLa-S3 | None | Ini1 | IgG-mus |
| HeLa-S3 | None | Input | IgG-mus |
| HeLa-S3 | None | Input | IgG-rab |
| HeLa-S3 | None | Input | Large_Fragment |
| HeLa-S3 | None | Input | MNase |
| HeLa-S3 | None | Input | Naked_DNA |
| HeLa-S3 | None | Input | std |
| HeLa-S3 | None | JunD | IgG-rab |
| HeLa-S3 | None | Max | std |
| HeLa-S3 | None | Nrf1 | IgG-mus |
| HeLa-S3 | None | Pol2 | std |
| HeLa-S3 | None | RPC155 | std |
| HeLa-S3 | None | TFIIIC-110 | std |
| HeLa-S3 | None | TR4 | std |
| HeLa-S3 | None | c-Fos | std |
| HeLa-S3 | None | c-Jun | IgG-rab |
| HeLa-S3 | None | c-Myc | std |
| HepG2 | forskolin | CEBPB | std |
| HepG2 | forskolin | ERRA | std |
| HepG2 | forskolin | GRp20 | std |
| HepG2 | forskolin | HNF4A | std |
| HepG2 | forskolin | HSF1 | std |
| HepG2 | forskolin | Input | std |
| HepG2 | forskolin | PGC1A | std |
| HepG2 | forskolin | Pol2 | std |
| HepG2 | insulin | Input | std |
| HepG2 | insulin | SREBP1 | std |
| HepG2 | pravastatin | Input | std |
| HepG2 | pravastatin | Pol2 | std |
| HepG2 | pravastatin | SREBP1 | std |
| HepG2 | pravastatin | SREBP2 | std |
| HepG2b | None | Input | UCDavis |
| HepG2b | None | TR4 | UCDavis |
| K562 | IFNa30 | Input | std |
| K562 | IFNa30 | Pol2 | std |
| K562 | IFNa30 | STAT1 | std |
| K562 | IFNa30 | STAT2 | std |
| K562 | IFNa30 | c-Myc | std |
| K562 | IFNa6h | Input | std |
| K562 | IFNa6h | Pol2 | std |
| K562 | IFNa6h | STAT1 | std |
| K562 | IFNa6h | STAT2 | std |
| K562 | IFNa6h | c-Jun | std |
| K562 | IFNa6h | c-Myc | std |
| K562 | IFNg30 | Input | std |
| K562 | IFNg30 | Pol2 | std |
| K562 | IFNg30 | STAT1 | std |
| K562 | IFNg30 | c-Jun | std |
| K562 | IFNg6h | Input | std |
| K562 | IFNg6h | Pol2 | std |
| K562 | IFNg6h | STAT1 | std |
| K562 | IFNg6h | c-Jun | std |
| K562 | IFNg6h | c-Myc | std |
| K562 | None | ATF3 | std |
| K562 | None | BDP1 | std |
| K562 | None | BRF1 | std |
| K562 | None | BRF2 | std |
| K562 | None | Brg1 | IgG-mus |
| K562 | None | GTF2B | std |
| K562 | None | Ini1 | IgG-mus |
| K562 | None | Input | IgG-mus |
| K562 | None | Input | std |
| K562 | None | JunD | std |
| K562 | None | Max | std |
| K562 | None | NELFe | std |
| K562 | None | NF-E2 | std |
| K562 | None | NF-YA | std |
| K562 | None | NF-YB | std |
| K562 | None | Pol2 | IgG-mus |
| K562 | None | Pol2 | std |
| K562 | None | Pol3 | std |
| K562 | None | RPC155 | std |
| K562 | None | Rad21 | std |
| K562 | None | SIRT6 | std |
| K562 | None | TFIIIC-110 | std |
| K562 | None | XRCC4 | std |
| K562 | None | c-Fos | std |
| K562 | None | c-Jun | std |
| K562 | None | c-Myc | std |
| K562b | None | E2F4 | UCDavis |
| K562b | None | E2F6 | UCDavis |
| K562b | None | GATA-1 | UCDavis |
| K562b | None | GATA-2 | UCDavis |
| K562b | None | Input | UCDavis |
| K562b | None | SETDB1 | MNase |
| K562b | None | SETDB1 | UCDavis |
| K562b | None | TR4 | UCDavis |
| K562b | None | YY1 | UCDavis |
| K562b | None | ZNF263 | UCDavis |
| K562b | None | ZNF274 | UCDavis |
| MCF-7 | None | HA-E2F1 | UCDavis |
| MCF-7 | None | Input | UCDavis |
| NB4 | None | Input | std |
| NB4 | None | Pol2 | std |
| NT2-D1 | None | Input | UCDavis |
| NT2-D1 | None | SUZ12 | UCDavis |
| NT2-D1 | None | YY1 | UCDavis |
+-----------+-------------+------------+----------------+
175 rows in set (0.14 sec)
mdbUpdate hg18 -vars="cell=GM18526 treatment=None antibody=NFKB input=IgG-mrabus" -var=input -val=IgG-rab -test
mdbPrint hg18 -vars="composite=wgEncodeYaleChIPseq" -ra > mdbYaleBefore.ra
insert into mdb_tdreszer (select t2.obj,"inputType",varType,val from mdb_tdreszer t2 where t2.obj like "wgEncodeYale%" and var = "input");
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq antibody=Input" -var=input -val=yes
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq antibody!=Input" -var=input -val=no
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM10847 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM10847/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM10847 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM10847/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM12878/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM12878/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Input inputType=std" -var=inputType -val=GM12878/None/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12891 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM12891/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12891 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM12891/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12892 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM12892/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12892 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM12892/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM15510 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM15510/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM15510 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM15510/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18505 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM18505/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18505 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM18505/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18526 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM18526/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18526 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM18526/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18951 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM18951/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18951 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM18951/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19099 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM19099/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19099 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM19099/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19193 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=GM19193/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19193 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=GM19193/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HCT-116 treatment=None antibody=Input inputType=UCDavis" -var=inputType -val=HCT-116/None/Input/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HEK293(b) treatment=None antibody=Input inputType=std" -var=inputType -val=HEK293(b)/None/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HUVEC treatment=None antibody=Input inputType=std" -var=inputType -val=HUVEC/None/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=IFNg30 antibody=Input inputType=std" -var=inputType -val=HeLa-S3/IFNg30/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=HeLa-S3/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Input inputType=IgG-rab" -var=inputType -val=HeLa-S3/None/Input/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Input inputType=Large_Fragment" -var=inputType -val=HeLa-S3/None/Input/Large_Fragment
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Input inputType=MNase" -var=inputType -val=HeLa-S3/None/Input/MNase
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Input inputType=Naked_DNA" -var=inputType -val=HeLa-S3/None/Input/Naked_DNA
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Input inputType=std" -var=inputType -val=HeLa-S3/None/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=Input inputType=std" -var=inputType -val=HepG2/forskolin/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=insulin antibody=Input inputType=std" -var=inputType -val=HepG2/insulin/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=pravastatin antibody=Input inputType=std" -var=inputType -val=HepG2/pravastatin/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2b treatment=None antibody=Input inputType=UCDavis" -var=inputType -val=HepG2b/None/Input/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa30 antibody=Input inputType=std" -var=inputType -val=K562/IFNa30/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa6h antibody=Input inputType=std" -var=inputType -val=K562/IFNa6h/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg30 antibody=Input inputType=std" -var=inputType -val=K562/IFNg30/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg6h antibody=Input inputType=std" -var=inputType -val=K562/IFNg6h/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Input inputType=IgG-mus" -var=inputType -val=K562/None/Input/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Input inputType=std" -var=inputType -val=K562/None/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=Input inputType=UCDavis" -var=inputType -val=K562b/None/Input/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=MCF-7 treatment=None antibody=Input inputType=UCDavis" -var=inputType -val=MCF-7/None/Input/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=NB4 treatment=None antibody=Input inputType=std" -var=inputType -val=NB4/None/Input/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=NT2-D1 treatment=None antibody=Input inputType=UCDavis" -var=inputType -val=NT2-D1/None/Input/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM10847 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM10847/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM10847 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM10847/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=JunD inputType=std" -var=inputType -val=GM12878/None/JunD/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Max inputType=std" -var=inputType -val=GM12878/None/Max/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM12878/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM12878/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Pol2 inputType=std" -var=inputType -val=GM12878/None/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Pol3 inputType=std" -var=inputType -val=GM12878/None/Pol3/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=Rad21inputType=IgG-rab" -var=inputType -val=GM12878/None/Rad21/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=TR4 inputType=std" -var=inputType -val=GM12878/None/TR4/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=YY1 inputType=std" -var=inputType -val=GM12878/None/YY1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=ZZZ3 inputType=std" -var=inputType -val=GM12878/None/ZZZ3/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=None antibody=c-FosinputType=std" -var=inputType -val=GM12878/None/c-Fos/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12878 treatment=TNFa antibody=NFKB inputType=std" -var=inputType -val=GM12878/TNFa/NFKB/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12891 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM12891/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12891 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM12891/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12892 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM12892/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM12892 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM12892/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM15510 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM15510/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM15510 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM15510/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18505 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM18505/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18505 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM18505/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18526 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM18526/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18526 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM18526/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18951 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM18951/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM18951 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM18951/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19099 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM19099/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19099 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM19099/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19193 treatment=None antibody=NFKB inputType=IgG-rab" -var=inputType -val=GM19193/None/NFKB/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=GM19193 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=GM19193/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HCT-116 treatment=None antibody=Pol2 inputType=UCDavis" -var=inputType -val=HCT-116/None/Pol2/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HCT-116 treatment=None antibody=TCF4 inputType=UCDavis" -var=inputType -val=HCT-116/None/TCF4/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HCT-116 treatment=None antibody=TCF7L2 inputType=UCDavis" -var=inputType -val=HCT-116/None/TCF7L2/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HEK293(b) treatment=None antibody=Pol2 inputType=std" -var=inputType -val=HEK293(b)/None/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HUVEC treatment=None antibody=Max inputType=std" -var=inputType -val=HUVEC/None/Max/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HUVEC treatment=None antibody=Pol2 inputType=std" -var=inputType -val=HUVEC/None/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HUVEC treatment=None antibody=c-Jun inputType=std" -var=inputType -val=HUVEC/None/c-Jun/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=IFNg antibody=STAT1 inputType=std" -var=inputType -val=HeLa-S3/IFNg/STAT1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=IFNg30 antibody=STAT1 inputType=std" -var=inputType -val=HeLa-S3/IFNg30/STAT1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=AP-2alpha inputType=std" -var=inputType -val=HeLa-S3/None/AP-2alpha/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=AP-2gamma inputType=std" -var=inputType -val=HeLa-S3/None/AP-2gamma/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=BAF155 inputType=IgG-mus" -var=inputType -val=HeLa-S3/None/BAF155/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=BAF170 inputType=IgG-mus" -var=inputType -val=HeLa-S3/None/BAF170/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=BDP1 inputType=std" -var=inputType -val=HeLa-S3/None/BDP1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=BRF1 inputType=std" -var=inputType -val=HeLa-S3/None/BRF1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=BRF2 inputType=std" -var=inputType -val=HeLa-S3/None/BRF2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Brg1 inputType=IgG-mus" -var=inputType -val=HeLa-S3/None/Brg1/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=E2F1 inputType=std" -var=inputType -val=HeLa-S3/None/E2F1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=E2F4 inputType=std" -var=inputType -val=HeLa-S3/None/E2F4/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=E2F6 inputType=std" -var=inputType -val=HeLa-S3/None/E2F6/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=HA-E2F1 inputType=std" -var=inputType -val=HeLa-S3/None/HA-E2F1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=HA-F2F1 inputType=std" -var=inputType -val=HeLa-S3/None/HA-F2F1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Ini1 inputType=IgG-mus" -var=inputType -val=HeLa-S3/None/Ini1/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=JunD inputType=IgG-rab" -var=inputType -val=HeLa-S3/None/JunD/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Max inputType=std" -var=inputType -val=HeLa-S3/None/Max/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Nrf1 inputType=IgG-mus" -var=inputType -val=HeLa-S3/None/Nrf1/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=Pol2 inputType=std" -var=inputType -val=HeLa-S3/None/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=RPC155 inputType=std" -var=inputType -val=HeLa-S3/None/RPC155/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=TFIIIC-110 inputType=std" -var=inputType -val=HeLa-S3/None/TFIIIC-110/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=TR4 inputType=std" -var=inputType -val=HeLa-S3/None/TR4/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=c-Fos inputType=std" -var=inputType -val=HeLa-S3/None/c-Fos/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=c-Jun inputType=IgG-rab" -var=inputType -val=HeLa-S3/None/c-Jun/IgG-rab
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HeLa-S3 treatment=None antibody=c-Myc inputType=std" -var=inputType -val=HeLa-S3/None/c-Myc/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=CEBPB inputType=std" -var=inputType -val=HepG2/forskolin/CEBPB/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=ERRA inputType=std" -var=inputType -val=HepG2/forskolin/ERRA/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=GRp20 inputType=std" -var=inputType -val=HepG2/forskolin/GRp20/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=HNF4A inputType=std" -var=inputType -val=HepG2/forskolin/HNF4A/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=HSF1 inputType=std" -var=inputType -val=HepG2/forskolin/HSF1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=PGC1A inputType=std" -var=inputType -val=HepG2/forskolin/PGC1A/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=forskolin antibody=Pol2 inputType=std" -var=inputType -val=HepG2/forskolin/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=insulin antibody=SREBP1 inputType=std" -var=inputType -val=HepG2/insulin/SREBP1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=pravastatin antibody=Pol2 inputType=std" -var=inputType -val=HepG2/pravastatin/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=pravastatin antibody=SREBP1 inputType=std" -var=inputType -val=HepG2/pravastatin/SREBP1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2 treatment=pravastatin antibody=SREBP2 inputType=std" -var=inputType -val=HepG2/pravastatin/SREBP2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=HepG2b treatment=None antibody=TR4 inputType=UCDavis" -var=inputType -val=HepG2b/None/TR4/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa30 antibody=Pol2 inputType=std" -var=inputType -val=K562/IFNa30/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa30 antibody=STAT1 inputType=std" -var=inputType -val=K562/IFNa30/STAT1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa30 antibody=STAT2 inputType=std" -var=inputType -val=K562/IFNa30/STAT2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa30 antibody=c-Myc inputType=std" -var=inputType -val=K562/IFNa30/c-Myc/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa6h antibody=Pol2 inputType=std" -var=inputType -val=K562/IFNa6h/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa6h antibody=STAT1 inputType=std" -var=inputType -val=K562/IFNa6h/STAT1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa6h antibody=STAT2 inputType=std" -var=inputType -val=K562/IFNa6h/STAT2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa6h antibody=c-Jun inputType=std" -var=inputType -val=K562/IFNa6h/c-Jun/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNa6h antibody=c-Myc inputType=std" -var=inputType -val=K562/IFNa6h/c-Myc/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg30 antibody=Pol2 inputType=std" -var=inputType -val=K562/IFNg30/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg30 antibody=STAT1 inputType=std" -var=inputType -val=K562/IFNg30/STAT1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg30 antibody=c-Jun inputType=std" -var=inputType -val=K562/IFNg30/c-Jun/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg6h antibody=Pol2 inputType=std" -var=inputType -val=K562/IFNg6h/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg6h antibody=STAT1 inputType=std" -var=inputType -val=K562/IFNg6h/STAT1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg6h antibody=c-Jun inputType=std" -var=inputType -val=K562/IFNg6h/c-Jun/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=IFNg6h antibody=c-Myc inputType=std" -var=inputType -val=K562/IFNg6h/c-Myc/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=ATF3 inputType=std" -var=inputType -val=K562/None/ATF3/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=BDP1 inputType=std" -var=inputType -val=K562/None/BDP1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=BRF1 inputType=std" -var=inputType -val=K562/None/BRF1/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=BRF2 inputType=std" -var=inputType -val=K562/None/BRF2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Brg1 inputType=IgG-mus" -var=inputType -val=K562/None/Brg1/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=GTF2B inputType=std" -var=inputType -val=K562/None/GTF2B/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Ini1 inputType=IgG-mus" -var=inputType -val=K562/None/Ini1/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=JunD inputType=std" -var=inputType -val=K562/None/JunD/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Max inputType=std" -var=inputType -val=K562/None/Max/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=NELFe inputType=std" -var=inputType -val=K562/None/NELFe/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=NF-E2 inputType=std" -var=inputType -val=K562/None/NF-E2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=NF-YA inputType=std" -var=inputType -val=K562/None/NF-YA/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=NF-YB inputType=std" -var=inputType -val=K562/None/NF-YB/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Pol2 inputType=IgG-mus" -var=inputType -val=K562/None/Pol2/IgG-mus
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Pol2 inputType=std" -var=inputType -val=K562/None/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Pol3 inputType=std" -var=inputType -val=K562/None/Pol3/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=RPC155 inputType=std" -var=inputType -val=K562/None/RPC155/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=Rad21 inputType=std" -var=inputType -val=K562/None/Rad21/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=SIRT6 inputType=std" -var=inputType -val=K562/None/SIRT6/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=TFIIIC-110 inputType=std" -var=inputType -val=K562/None/TFIIIC-110/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=XRCC4 inputType=std" -var=inputType -val=K562/None/XRCC4/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=c-Fos inputType=std" -var=inputType -val=K562/None/c-Fos/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=c-Jun inputType=std" -var=inputType -val=K562/None/c-Jun/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562 treatment=None antibody=c-Myc inputType=std" -var=inputType -val=K562/None/c-Myc/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=E2F4 inputType=UCDavis" -var=inputType -val=K562b/None/E2F4/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=E2F6 inputType=UCDavis" -var=inputType -val=K562b/None/E2F6/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=GATA-1 inputType=UCDavis" -var=inputType -val=K562b/None/GATA-1/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=GATA-2 inputType=UCDavis" -var=inputType -val=K562b/None/GATA-2/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=SETDB1 inputType=MNase" -var=inputType -val=K562b/None/SETDB1/MNase
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=SETDB1 inputType=UCDavis" -var=inputType -val=K562b/None/SETDB1/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=TR4 inputType=UCDavis" -var=inputType -val=K562b/None/TR4/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=YY1 inputType=UCDavis" -var=inputType -val=K562b/None/YY1/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=ZNF263 inputType=UCDavis" -var=inputType -val=K562b/None/ZNF263/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=K562b treatment=None antibody=ZNF274 inputType=UCDavis" -var=inputType -val=K562b/None/ZNF274/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=MCF-7 treatment=None antibody=HA-E2F1 inputType=UCDavis" -var=inputType -val=MCF-7/None/HA-E2F1/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=NB4 treatment=None antibody=Pol2 inputType=std" -var=inputType -val=NB4/None/Pol2/std
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=NT2-D1 treatment=None antibody=SUZ12 inputType=UCDavis" -var=inputType -val=NT2-D1/None/SUZ12/UCDavis
mdbUpdate hg18 -vars="composite=wgEncodeYaleChIPseq cell=NT2-D1 treatment=None antibody=YY1 inputType=UCDavis" -var=inputType -val=NT2-D1/None/YY1/UCDavis
### Note: had to do some manual changes
select distinct t1.val cell,t2.val treatment,t3.val antibody,t4.val input,t5.val inputType from mdb_tdreszer t1,mdb_tdreszer t2,mdb_tdreszer t3,mdb_tdreszer t4,mdb_tdreszer t5 where t1.obj like "wgEncodeYaleChIP%"
and t1.obj = t2.obj and t2.obj = t3.obj and t3.obj = t4.obj and t4.obj = t5.obj
and t1.var = "cell" and t2.var = "treatment" and t3.var = "antibody" and t4.var = "input" and t5.var = "inputType"
order by t5.val,t4.val,t1.val,t2.val,t3.val;
+-----------+-------------+------------+-------+-----------------------------------+
| cell | treatment | antibody | input | inputType |
+-----------+-------------+------------+-------+-----------------------------------+
| GM10847 | None | Pol2 | no | GM10847/None/Input/IgG-mus |
| GM10847 | None | Input | yes | GM10847/None/Input/IgG-mus |
| GM10847 | None | NFKB | no | GM10847/None/Input/IgG-rab |
| GM10847 | None | Input | yes | GM10847/None/Input/IgG-rab |
| GM12878 | None | Pol2 | no | GM12878/None/Input/IgG-mus |
| GM12878 | None | Input | yes | GM12878/None/Input/IgG-mus |
| GM12878 | None | NFKB | no | GM12878/None/Input/IgG-rab |
| GM12878 | None | Rad21 | no | GM12878/None/Input/IgG-rab |
| GM12878 | None | Input | yes | GM12878/None/Input/IgG-rab |
| GM12878 | None | JunD | no | GM12878/None/Input/std |
| GM12878 | None | Max | no | GM12878/None/Input/std |
| GM12878 | None | Pol2 | no | GM12878/None/Input/std |
| GM12878 | None | Pol3 | no | GM12878/None/Input/std |
| GM12878 | None | TR4 | no | GM12878/None/Input/std |
| GM12878 | None | YY1 | no | GM12878/None/Input/std |
| GM12878 | None | ZZZ3 | no | GM12878/None/Input/std |
| GM12878 | None | c-Fos | no | GM12878/None/Input/std |
| GM12878 | None | Input | yes | GM12878/None/Input/std |
| GM12878 | TNFa | NFKB | no | GM12878/TNFa/Input/std |
| GM12891 | None | Pol2 | no | GM12891/None/Input/IgG-mus |
| GM12891 | None | Input | yes | GM12891/None/Input/IgG-mus |
| GM12891 | None | NFKB | no | GM12891/None/Input/IgG-rab |
| GM12891 | None | Input | yes | GM12891/None/Input/IgG-rab |
| GM12892 | None | Pol2 | no | GM12892/None/Input/IgG-mus |
| GM12892 | None | Input | yes | GM12892/None/Input/IgG-mus |
| GM12892 | None | NFKB | no | GM12892/None/Input/IgG-rab |
| GM12892 | None | Input | yes | GM12892/None/Input/IgG-rab |
| GM15510 | None | Pol2 | no | GM15510/None/Input/IgG-mus |
| GM15510 | None | Input | yes | GM15510/None/Input/IgG-mus |
| GM15510 | None | NFKB | no | GM15510/None/Input/IgG-rab |
| GM15510 | None | Input | yes | GM15510/None/Input/IgG-rab |
| GM18505 | None | Pol2 | no | GM18505/None/Input/IgG-mus |
| GM18505 | None | Input | yes | GM18505/None/Input/IgG-mus |
| GM18505 | None | NFKB | no | GM18505/None/Input/IgG-rab |
| GM18505 | None | Input | yes | GM18505/None/Input/IgG-rab |
| GM18526 | None | Pol2 | no | GM18526/None/Input/IgG-mus |
| GM18526 | None | Input | yes | GM18526/None/Input/IgG-mus |
| GM18526 | None | NFKB | no | GM18526/None/Input/IgG-rab |
| GM18526 | None | Input | yes | GM18526/None/Input/IgG-rab |
| GM18951 | None | Pol2 | no | GM18951/None/Input/IgG-mus |
| GM18951 | None | Input | yes | GM18951/None/Input/IgG-mus |
| GM18951 | None | NFKB | no | GM18951/None/Input/IgG-rab |
| GM18951 | None | Input | yes | GM18951/None/Input/IgG-rab |
| GM19099 | None | Pol2 | no | GM19099/None/Input/IgG-mus |
| GM19099 | None | Input | yes | GM19099/None/Input/IgG-mus |
| GM19099 | None | NFKB | no | GM19099/None/Input/IgG-rab |
| GM19099 | None | Input | yes | GM19099/None/Input/IgG-rab |
| GM19193 | None | Pol2 | no | GM19193/None/Input/IgG-mus |
| GM19193 | None | Input | yes | GM19193/None/Input/IgG-mus |
| GM19193 | None | NFKB | no | GM19193/None/Input/IgG-rab |
| GM19193 | None | Input | yes | GM19193/None/Input/IgG-rab |
| HCT-116 | None | Pol2 | no | HCT-116/None/Input/UCDavis |
| HCT-116 | None | TCF4 | no | HCT-116/None/Input/UCDavis |
| HCT-116 | None | TCF7L2 | no | HCT-116/None/Input/UCDavis |
| HCT-116 | None | Input | yes | HCT-116/None/Input/UCDavis |
| HEK293(b) | None | Pol2 | no | HEK293/None/Input/std |
| HEK293(b) | None | Input | yes | HEK293/None/Input/std |
| HUVEC | None | Max | no | HUVEC/None/Input/std |
| HUVEC | None | Pol2 | no | HUVEC/None/Input/std |
| HUVEC | None | c-Jun | no | HUVEC/None/Input/std |
| HUVEC | None | Input | yes | HUVEC/None/Input/std |
| HeLa-S3 | IFNg | STAT1 | no | HeLa-S3/IFNg/Input/std |
| HeLa-S3 | IFNg30 | STAT1 | no | HeLa-S3/IFNg30/Input/std |
| HeLa-S3 | IFNg30 | Input | yes | HeLa-S3/IFNg30/Input/std |
| HeLa-S3 | None | BAF155 | no | HeLa-S3/None/Input/IgG-mus |
| HeLa-S3 | None | BAF170 | no | HeLa-S3/None/Input/IgG-mus |
| HeLa-S3 | None | Brg1 | no | HeLa-S3/None/Input/IgG-mus |
| HeLa-S3 | None | Ini1 | no | HeLa-S3/None/Input/IgG-mus |
| HeLa-S3 | None | Nrf1 | no | HeLa-S3/None/Input/IgG-mus |
| HeLa-S3 | None | Input | yes | HeLa-S3/None/Input/IgG-mus |
| HeLa-S3 | None | JunD | no | HeLa-S3/None/Input/IgG-rab |
| HeLa-S3 | None | c-Jun | no | HeLa-S3/None/Input/IgG-rab |
| HeLa-S3 | None | Input | yes | HeLa-S3/None/Input/IgG-rab |
| HeLa-S3 | None | Input | yes | HeLa-S3/None/Input/Large_Fragment |
| HeLa-S3 | None | Input | yes | HeLa-S3/None/Input/MNase |
| HeLa-S3 | None | Input | yes | HeLa-S3/None/Input/Naked_DNA |
| HeLa-S3 | None | AP-2alpha | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | AP-2gamma | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | BDP1 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | BRF1 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | BRF2 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | E2F1 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | E2F4 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | E2F6 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | HA-E2F1 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | HA-F2F1 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | Max | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | Pol2 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | RPC155 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | TFIIIC-110 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | TR4 | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | c-Fos | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | c-Myc | no | HeLa-S3/None/Input/std |
| HeLa-S3 | None | Input | yes | HeLa-S3/None/Input/std |
| HepG2 | forskolin | CEBPB | no | HepG2/forskolin/CEBPB/std |
| HepG2 | forskolin | ERRA | no | HepG2/forskolin/ERRA/std |
| HepG2 | forskolin | GRp20 | no | HepG2/forskolin/Input/std |
| HepG2 | forskolin | HNF4A | no | HepG2/forskolin/Input/std |
| HepG2 | forskolin | HSF1 | no | HepG2/forskolin/Input/std |
| HepG2 | forskolin | PGC1A | no | HepG2/forskolin/Input/std |
| HepG2 | forskolin | Pol2 | no | HepG2/forskolin/Input/std |
| HepG2 | forskolin | Input | yes | HepG2/forskolin/Input/std |
| HepG2 | insulin | SREBP1 | no | HepG2/insulin/Input/std |
| HepG2 | insulin | Input | yes | HepG2/insulin/Input/std |
| HepG2 | pravastatin | SREBP2 | no | HepG2/pravastatin//std |
| HepG2 | pravastatin | Pol2 | no | HepG2/pravastatin/Input/std |
| HepG2 | pravastatin | SREBP1 | no | HepG2/pravastatin/Input/std |
| HepG2 | pravastatin | Input | yes | HepG2/pravastatin/Input/std |
| HepG2b | None | TR4 | no | HepG2b/None/Input/UCDavis |
| HepG2b | None | Input | yes | HepG2b/None/Input/UCDavis |
| K562 | IFNa30 | Pol2 | no | K562/IFNa30/Input/std |
| K562 | IFNa30 | STAT1 | no | K562/IFNa30/Input/std |
| K562 | IFNa30 | STAT2 | no | K562/IFNa30/Input/std |
| K562 | IFNa30 | c-Myc | no | K562/IFNa30/Input/std |
| K562 | IFNa30 | Input | yes | K562/IFNa30/Input/std |
| K562 | IFNa6h | Pol2 | no | K562/IFNa6h/Input/std |
| K562 | IFNa6h | STAT1 | no | K562/IFNa6h/Input/std |
| K562 | IFNa6h | STAT2 | no | K562/IFNa6h/Input/std |
| K562 | IFNa6h | c-Jun | no | K562/IFNa6h/Input/std |
| K562 | IFNa6h | c-Myc | no | K562/IFNa6h/Input/std |
| K562 | IFNa6h | Input | yes | K562/IFNa6h/Input/std |
| K562 | IFNg30 | Pol2 | no | K562/IFNg30/Input/std |
| K562 | IFNg30 | STAT1 | no | K562/IFNg30/Input/std |
| K562 | IFNg30 | c-Jun | no | K562/IFNg30/Input/std |
| K562 | IFNg30 | Input | yes | K562/IFNg30/Input/std |
| K562 | IFNg6h | Pol2 | no | K562/IFNg6h/Input/std |
| K562 | IFNg6h | STAT1 | no | K562/IFNg6h/Input/std |
| K562 | IFNg6h | c-Jun | no | K562/IFNg6h/Input/std |
| K562 | IFNg6h | c-Myc | no | K562/IFNg6h/Input/std |
| K562 | IFNg6h | Input | yes | K562/IFNg6h/Input/std |
| K562 | None | Brg1 | no | K562/None/Input/IgG-mus |
| K562 | None | Ini1 | no | K562/None/Input/IgG-mus |
| K562 | None | Input | yes | K562/None/Input/IgG-mus |
| K562 | None | ATF3 | no | K562/None/Input/std |
| K562 | None | BDP1 | no | K562/None/Input/std |
| K562 | None | BRF1 | no | K562/None/Input/std |
| K562 | None | BRF2 | no | K562/None/Input/std |
| K562 | None | GTF2B | no | K562/None/Input/std |
| K562 | None | JunD | no | K562/None/Input/std |
| K562 | None | Max | no | K562/None/Input/std |
| K562 | None | NELFe | no | K562/None/Input/std |
| K562 | None | NF-E2 | no | K562/None/Input/std |
| K562 | None | NF-YA | no | K562/None/Input/std |
| K562 | None | NF-YB | no | K562/None/Input/std |
| K562 | None | Pol2 | no | K562/None/Input/std |
| K562 | None | Pol3 | no | K562/None/Input/std |
| K562 | None | RPC155 | no | K562/None/Input/std |
| K562 | None | Rad21 | no | K562/None/Input/std |
| K562 | None | SIRT6 | no | K562/None/Input/std |
| K562 | None | TFIIIC-110 | no | K562/None/Input/std |
| K562 | None | XRCC4 | no | K562/None/Input/std |
| K562 | None | c-Fos | no | K562/None/Input/std |
| K562 | None | c-Jun | no | K562/None/Input/std |
| K562 | None | c-Myc | no | K562/None/Input/std |
| K562 | None | Input | yes | K562/None/Input/std |
| K562 | None | Pol2 | no | K562/None/Pol2/IgG-mus |
| K562b | None | SETDB1 | no | K562b/None/Input/MNase |
| K562b | None | E2F4 | no | K562b/None/Input/UCDavis |
| K562b | None | E2F6 | no | K562b/None/Input/UCDavis |
| K562b | None | GATA-1 | no | K562b/None/Input/UCDavis |
| K562b | None | GATA-2 | no | K562b/None/Input/UCDavis |
| K562b | None | SETDB1 | no | K562b/None/Input/UCDavis |
| K562b | None | TR4 | no | K562b/None/Input/UCDavis |
| K562b | None | YY1 | no | K562b/None/Input/UCDavis |
| K562b | None | ZNF263 | no | K562b/None/Input/UCDavis |
| K562b | None | ZNF274 | no | K562b/None/Input/UCDavis |
| K562b | None | Input | yes | K562b/None/Input/UCDavis |
| MCF-7 | None | HA-E2F1 | no | MCF-7/None/Input/UCDavis |
| MCF-7 | None | Input | yes | MCF-7/None/Input/UCDavis |
| NB4 | None | Pol2 | no | NB4/None/Input/std |
| NB4 | None | Input | yes | NB4/None/Input/std |
| NT2-D1 | None | SUZ12 | no | NT2-D1/None/Input/UCDavis |
| NT2-D1 | None | YY1 | no | NT2-D1/None/Input/UCDavis |
| NT2-D1 | None | Input | yes | NT2-D1/None/Input/UCDavis |
+-----------+-------------+------------+-------+-----------------------------------+
174 rows in set (0.23 sec)
select distinct val from mdb_tdreszer where obj like "wgEncodeYaleChIP%" and var = "inputType";
52 rows in set (0.02 sec)
select distinct t2.val from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj = t2.obj and t1.obj like "wgEncodeYaleChIP%" and t1.var = "input" and t1.val = "yes" and t2.var = "inputType";
45 rows in set (0.02 sec)
select distinct t1.val input,t2.val inputType from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj = t2.obj and t1.obj like "wgEncodeYaleChIP%" and t1.var = "input" and t2.var = "inputType" order by t2.val, t1.val;
### Differences ?
+-------+-----------------------------------+
| no | GM12878/TNFa/Input/std |
| no | HeLa-S3/IFNg/Input/std |
| yes | HeLa-S3/None/Input/Large_Fragment |
| yes | HeLa-S3/None/Input/MNase |
| yes | HeLa-S3/None/Input/Naked_DNA |
| no | HepG2/forskolin/CEBPB/std |
| no | HepG2/forskolin/ERRA/std |
| no | HepG2/pravastatin//std | | no | HepG2/pravastatin/Input/std |
| no | K562/None/Pol2/IgG-mus |
| no | K562b/None/Input/MNase |
+-------+-----------------------------------+
select distinct val from mdb_tdreszer where obj like "wgEncodeYaleChIP%" and var = "inputType";
46 rows in set (0.02 sec)
select distinct t2.val from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj = t2.obj and t1.obj like "wgEncodeYaleChIP%" and t1.var = "input" and t1.val = "yes" and t2.var = "inputType";
45 rows in set (0.02 sec)
select distinct t1.val input,t2.val inputType from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj = t2.obj and t1.obj like "wgEncodeYaleChIP%" and t1.var = "input" and t2.var = "inputType" order by t2.val, t1.val;
+-------+-----------------------------------+
| input | inputType |
+-------+-----------------------------------+
| no | GM10847/None/Input/IgG-mus |
| yes | GM10847/None/Input/IgG-mus |
| no | GM10847/None/Input/IgG-rab |
| yes | GM10847/None/Input/IgG-rab |
| no | GM12878/None/Input/IgG-mus |
| yes | GM12878/None/Input/IgG-mus |
| no | GM12878/None/Input/IgG-rab |
| yes | GM12878/None/Input/IgG-rab |
| no | GM12878/None/Input/std |
| yes | GM12878/None/Input/std |
| no | GM12891/None/Input/IgG-mus |
| yes | GM12891/None/Input/IgG-mus |
| no | GM12891/None/Input/IgG-rab |
| yes | GM12891/None/Input/IgG-rab |
| no | GM12892/None/Input/IgG-mus |
| yes | GM12892/None/Input/IgG-mus |
| no | GM12892/None/Input/IgG-rab |
| yes | GM12892/None/Input/IgG-rab |
| no | GM15510/None/Input/IgG-mus |
| yes | GM15510/None/Input/IgG-mus |
| no | GM15510/None/Input/IgG-rab |
| yes | GM15510/None/Input/IgG-rab |
| no | GM18505/None/Input/IgG-mus |
| yes | GM18505/None/Input/IgG-mus |
| no | GM18505/None/Input/IgG-rab |
| yes | GM18505/None/Input/IgG-rab |
| no | GM18526/None/Input/IgG-mus |
| yes | GM18526/None/Input/IgG-mus |
| no | GM18526/None/Input/IgG-rab |
| yes | GM18526/None/Input/IgG-rab |
| no | GM18951/None/Input/IgG-mus |
| yes | GM18951/None/Input/IgG-mus |
| no | GM18951/None/Input/IgG-rab |
| yes | GM18951/None/Input/IgG-rab |
| no | GM19099/None/Input/IgG-mus |
| yes | GM19099/None/Input/IgG-mus |
| no | GM19099/None/Input/IgG-rab |
| yes | GM19099/None/Input/IgG-rab |
| no | GM19193/None/Input/IgG-mus |
| yes | GM19193/None/Input/IgG-mus |
| no | GM19193/None/Input/IgG-rab |
| yes | GM19193/None/Input/IgG-rab |
| no | HCT-116/None/Input/UCDavis |
| yes | HCT-116/None/Input/UCDavis |
| no | HEK293/None/Input/std |
| yes | HEK293/None/Input/std |
| no | HUVEC/None/Input/std |
| yes | HUVEC/None/Input/std |
| no | HeLa-S3/IFNg30/Input/std |
| yes | HeLa-S3/IFNg30/Input/std |
| no | HeLa-S3/None/Input/IgG-mus |
| yes | HeLa-S3/None/Input/IgG-mus |
| no | HeLa-S3/None/Input/IgG-rab |
| yes | HeLa-S3/None/Input/IgG-rab |
| yes | HeLa-S3/None/Input/Large_Fragment |
| yes | HeLa-S3/None/Input/MNase |
| yes | HeLa-S3/None/Input/Naked_DNA |
| no | HeLa-S3/None/Input/std |
| yes | HeLa-S3/None/Input/std |
| no | HepG2/forskolin/Input/std |
| yes | HepG2/forskolin/Input/std |
| no | HepG2/insulin/Input/std |
| yes | HepG2/insulin/Input/std |
| no | HepG2/pravastatin/Input/std |
| yes | HepG2/pravastatin/Input/std |
| no | HepG2b/None/Input/UCDavis |
| yes | HepG2b/None/Input/UCDavis |
| no | K562/IFNa30/Input/std |
| yes | K562/IFNa30/Input/std |
| no | K562/IFNa6h/Input/std |
| yes | K562/IFNa6h/Input/std |
| no | K562/IFNg30/Input/std |
| yes | K562/IFNg30/Input/std |
| no | K562/IFNg6h/Input/std |
| yes | K562/IFNg6h/Input/std |
| no | K562/None/Input/IgG-mus |
| yes | K562/None/Input/IgG-mus |
| no | K562/None/Input/std |
| yes | K562/None/Input/std |
| no | K562b/None/Input/MNase |
| no | K562b/None/Input/UCDavis |
| yes | K562b/None/Input/UCDavis |
| no | MCF-7/None/Input/UCDavis |
| yes | MCF-7/None/Input/UCDavis |
| no | NB4/None/Input/std |
| yes | NB4/None/Input/std |
| no | NT2-D1/None/Input/UCDavis |
| yes | NT2-D1/None/Input/UCDavis |
+-------+-----------------------------------+
88 rows in set (0.09 sec)
### Differences ?
+-------+-----------------------------------+
| yes | HeLa-S3/None/Input/Large_Fragment |
| yes | HeLa-S3/None/Input/MNase |
| yes | HeLa-S3/None/Input/Naked_DNA |
| no | K562b/None/Input/MNase | ### This is a problem. Farnham should comment
+-------+-----------------------------------+
mdbPrint hg18 -vars="composite=wgEncodeYaleChIPseq" -ra > mdbYaleTfbs.ra
mdbUpdate hg18 -table=mdb mdbYaleTfbs.ra
cvs ci -m "Fixed Yale Inputs to match the HAIB model allowing pairing of exp.inputType = inp.inputType" mdbYaleTfbs.ra
### Need to add 'control' term in to replace removed 'input'. This is because Yale's experiments need 4 vars to be defined
mdbUpdate hg18 -vars="grant=Snyder inputType=%std" -var=control -val=std -test
mdbUpdate hg18 -vars="grant=Snyder inputType=%UCDavis" -var=control -val=UCDavis -test
mdbUpdate hg18 -vars="grant=Snyder inputType=%MNase" -var=control -val=MNase -test
mdbUpdate hg18 -vars="grant=Snyder inputType=%IgG-mus" -var=control -val=IgG-mus -test
mdbUpdate hg18 -vars="grant=Snyder inputType=%IgG-rab" -var=control -val=IgG-rab -test
mdbUpdate hg18 -vars="grant=Snyder inputType=%Naked_DNA" -var=control -val=Naked_DNA -test
mdbUpdate hg18 -vars="grant=Snyder inputType=%Large_Fragment" -var=control -val=Large_Fragment -test
Command would affected 559 row(s) in hg18.mdb_tdreszer
Command would affected 108 row(s) in hg18.mdb_tdreszer
Command would affected 11 row(s) in hg18.mdb_tdreszer
Command would affected 215 row(s) in hg18.mdb_tdreszer
Command would affected 167 row(s) in hg18.mdb_tdreszer
Command would affected 7 row(s) in hg18.mdb_tdreszer
Command would affected 6 row(s) in hg18.mdb_tdreszer
1073!
mdbUpdate hg18 -vars="grant=Snyder inputType=%std" -var=control -val=std
mdbUpdate hg18 -vars="grant=Snyder inputType=%UCDavis" -var=control -val=UCDavis
mdbUpdate hg18 -vars="grant=Snyder inputType=%MNase" -var=control -val=MNase
mdbUpdate hg18 -vars="grant=Snyder inputType=%IgG-mus" -var=control -val=IgG-mus
mdbUpdate hg18 -vars="grant=Snyder inputType=%IgG-rab" -var=control -val=IgG-rab
mdbUpdate hg18 -vars="grant=Snyder inputType=%Naked_DNA" -var=control -val=Naked_DNA
mdbUpdate hg18 -vars="grant=Snyder inputType=%Large_Fragment" -var=control -val=Large_Fragment
mdbPrint hg18 -vars="grant=Snyder" -ra > mdbYaleTfbs.ra
mdbUpdate hg18 -table=mdb mdbYaleTfbs.ra
cvs ci mdbYaleTfbs.ra
## Fix at last K562b/None/SETDB1/MNase
# MNase in this case is a treatment (sort of)!
# Register a treatment MNaseD (MNase is a control term!)
mdbPrint hg18 -vars="grant=Snyder cell=K562b treatment=None antibody=SETDB1 inputType=%MNase" > tmpMNase.ra
mdbUpdate hg18 -vars="grant=Snyder cell=K562b treatment=None antibody=SETDB1 inputType=%MNase" -var=treatment -val=MNaseD -test
mdbUpdate hg18 -vars="grant=Snyder cell=K562b treatment=MNaseD antibody=SETDB1 inputType=%MNase" -var=inputType -val=K562b/None/Input/UCDavis -test
mdbUpdate hg18 -vars="grant=Snyder cell=K562b treatment=MNaseD antibody=SETDB1" -var=control -val=UCDavis -test
mdbPrint hg18 -vars="grant=Snyder cell=K562b treatment=MNaseD antibody=SETDB1" > tmpMNase2.ra
diff tmpMNase.ra tmpMNase2.ra
mdbPrint hg18 -vars="grant=Snyder" > mdbYaleTfbs.ra
Using table named 'hg18.mdb_tdreszer'.
objects:1073 vars:22410
mdbUpdate hg18 -table=mdb mdbYaleTfbs.ra
Using table named 'hg18.mdb_tdreszer'.
Read 1073 metadata objects from hg18
Affected 0 row(s) in hg18.mdb_tdreszer
cvs ci -m "Straightened out Yale K562/None/SETDB1/MNase at last" mdbYaleTfbs.ra
# Peggy Farnham: "I'm happy!"
FIXME:
1) Need to alter make to generate shared mdb off of the mdb*.ra files
Necessary? I don't think so as long as users update shared mdb and mdb gets pushed to bta, public.
But doing this with makefile should ensure that mdb.ra files get checked in.
2) Need an exp table (autoincrement,"cell-GM12878 treatment=None antibody=CTCF control=std")
### Matrix too large:
http://www.dotnetoutsource.com/Download/jQuery_FixedTable/JQuery_FixedTable.aspx
2010-05-26 Released the big one
===============================
select db,id,name,status,user_id from projects where user_id = 39 and db = 'hg18' and status = 'reviewing';
+------+------+--------------------------------+-----------+---------+
| db | id | name | status | user_id |
+------+------+--------------------------------+-----------+---------+
| hg18 | 633 | YDH_tagAlign_update_v3 | reviewing | 39 |
| hg18 | 634 | YDH_tagAlign_update | reviewing | 39 |
| hg18 | 669 | YDH_K562_Pol3 | reviewing | 39 |
| hg18 | 739 | YDH_HeLa-S3_E2F6 | reviewing | 39 |
| hg18 | 757 | YDH_MCF-7_HA-E2F1 | reviewing | 39 |
| hg18 | 787 | YDH_tagAlign_update2 | reviewing | 39 |
| hg18 | 853 | YDH_GM12878_YY1 | reviewing | 39 |
| hg18 | 860 | YDH_K562b_ZNF274 | reviewing | 39 |
| hg18 | 861 | YDH_GM10847_IgG_Control | reviewing | 39 |
| hg18 | 862 | YDH_GM10847_IgG_Pol2 | reviewing | 39 |
| hg18 | 863 | YDH_GM12891_IgG_Control | reviewing | 39 |
| hg18 | 864 | YDH_K562_IgG_Control | reviewing | 39 |
| hg18 | 865 | YDH_GM12891_IgG_Pol2 | reviewing | 39 |
| hg18 | 996 | YDH_GM15510_IgG_Control | reviewing | 39 |
| hg18 | 997 | YDH_GM15510_IgG_Pol2 | reviewing | 39 |
| hg18 | 974 | YDH_K562_IFNg30_Pol2 | reviewing | 39 |
| hg18 | 1108 | YDH_GM10847_Rabbit_IgG | reviewing | 39 |
| hg18 | 1109 | YDH_GM12878_Rabbit_IgG | reviewing | 39 |
| hg18 | 1110 | YDH_GM12892_Rabbit_IgG | reviewing | 39 |
| hg18 | 1111 | YDH_GM12891_Rabbit_IgG | reviewing | 39 |
| hg18 | 1112 | YDH_GM15510_Rabbit_IgG | reviewing | 39 |
| hg18 | 1113 | YDH_GM18505_Rabbit_IgG | reviewing | 39 |
| hg18 | 1114 | YDH_GM18526_Rabbit_IgG | reviewing | 39 |
| hg18 | 1115 | YDH_GM18951_Rabbit_IgG | reviewing | 39 |
| hg18 | 1116 | YDH_GM19099_Rabbit_IgG | reviewing | 39 |
| hg18 | 1117 | YDH_GM19193_Rabbit_IgG | reviewing | 39 |
| hg18 | 1118 | YDH_HUVEC_IgG_Control | reviewing | 39 |
| hg18 | 1119 | YDH_HeLa_Brg1 | reviewing | 39 |
| hg18 | 1090 | YDH_MCF-7_Input | reviewing | 39 |
| hg18 | 1085 | YDH_HUVEC_Max | reviewing | 39 |
| hg18 | 1086 | YDH_HeLa-S3_Brf1 | reviewing | 39 |
| hg18 | 1087 | YDH_HeLa-S3_Brf2 | reviewing | 39 |
| hg18 | 1088 | YDH_K562b_MNase_SetDB1 | reviewing | 39 |
| hg18 | 1081 | YDH_K562_TFIIIC | reviewing | 39 |
| hg18 | 1082 | YDH_HeLa-S3_RPC155 | reviewing | 39 |
| hg18 | 1083 | YDH_K562_Brf2 | reviewing | 39 |
| hg18 | 1078 | YDH_HeLa-S3_Bdp1 | reviewing | 39 |
| hg18 | 1077 | YDH_HeLa-S3_TFIIIC | reviewing | 39 |
| hg18 | 1076 | YDH_GM12878_Rad21 | reviewing | 39 |
| hg18 | 1073 | YHD_HepG2_Insulin_SREBP1 | reviewing | 39 |
| hg18 | 1069 | YHD_HepG2_Forskolin_HSF1 | reviewing | 39 |
| hg18 | 1070 | YHD_HepG2_Insulin_Control | reviewing | 39 |
| hg18 | 1071 | YHD_HepG2_Forskolin_PGC1A | reviewing | 39 |
| hg18 | 1072 | YHD_HepG2_Forskolin_Pol2 | reviewing | 39 |
| hg18 | 1066 | YHD_HepG2_Forskolin_Control | reviewing | 39 |
| hg18 | 1067 | YHD_HepG2_Forskolin_GRp20 | reviewing | 39 |
| hg18 | 1068 | YHD_HepG2_Forskolin_HNF4A | reviewing | 39 |
| hg18 | 1063 | YHD_HepG2_Forskolin_ERRA | reviewing | 39 |
| hg18 | 1062 | YDH_HepG2_Forskolin_CEBPB | reviewing | 39 |
| hg18 | 1058 | YDH_K562_IFNg30_STAT1 | reviewing | 39 |
| hg18 | 1059 | YDH_K562_IFNg6h_STAT1 | reviewing | 39 |
| hg18 | 1051 | YDH_GM12891_IgG_NFKB | reviewing | 39 |
| hg18 | 1052 | YDH_GM15510_IgG_NFKB | reviewing | 39 |
| hg18 | 1053 | YDH_GM18951_IgG_NFKB | reviewing | 39 |
| hg18 | 1048 | YDH_GM19193_IgG_Pol2 | reviewing | 39 |
| hg18 | 1050 | YDH_GM10847_IgG_NFKB | reviewing | 39 |
| hg18 | 1047 | YDH_GM19193_IgG_Control | reviewing | 39 |
| hg18 | 1044 | YDH_GM18951_IgG_Control | reviewing | 39 |
| hg18 | 1045 | YDH_GM19099_IgG_Control | reviewing | 39 |
| hg18 | 1046 | YDH_GM19099_IgG_Pol2 | reviewing | 39 |
| hg18 | 1031 | YDH_HeLa-S3_IgG_Rabbit_c-Jun | reviewing | 39 |
| hg18 | 1032 | YDH_HeLa-S3_IgG_Rabbit_JunD | reviewing | 39 |
| hg18 | 1029 | YDH_GM18951_IgG_Pol2 | reviewing | 39 |
| hg18 | 1030 | YDH_HeLa-S3_IgG_Rabbit_Control | reviewing | 39 |
| hg18 | 1025 | YDH_GM18526_IgG_Control | reviewing | 39 |
| hg18 | 1024 | YDH_GM18526_IgG_Pol2 | reviewing | 39 |
| hg18 | 1020 | YHD_GM18505_IgG_Control | reviewing | 39 |
| hg18 | 1016 | YDH_GM18505_IgG_Pol2 | reviewing | 39 |
| hg18 | 1008 | YDH_GM12892_IgG_Pol2 | reviewing | 39 |
| hg18 | 999 | YDH_HeLa-S3_IgG_Nrf1 | reviewing | 39 |
| hg18 | 995 | YDH_HUVEC_Jun | reviewing | 39 |
| hg18 | 975 | YDH_K562_GTF2B | reviewing | 39 |
| hg18 | 888 | YDH_HeLa-S3_IgG_BAF155 | reviewing | 39 |
| hg18 | 890 | YDH_HeLa-S3_IgG_BAF170 | reviewing | 39 |
| hg18 | 892 | YDH_HeLa-S3_IgG_Ini1 | reviewing | 39 |
| hg18 | 893 | YDH_K562_IgG_Brg1 | reviewing | 39 |
| hg18 | 894 | YDH_K562_IgG_Ini1 | reviewing | 39 |
| hg18 | 895 | YDH_K562_IgG_Pol2 | reviewing | 39 |
| hg18 | 900 | YDH_GM12878_TR4 | reviewing | 39 |
| hg18 | 928 | YDH_HeLa-S3_E2F1 | reviewing | 39 |
| hg18 | 933 | YDH_GM12878_ZZZ3 | reviewing | 39 |
| hg18 | 941 | YDH_GM12892_IgG_NFKB | reviewing | 39 |
| hg18 | 942 | YDH_GM18526_IgG_NFKB | reviewing | 39 |
| hg18 | 943 | YDH_GM12878_IgG_NFKB | reviewing | 39 |
| hg18 | 945 | YDH_GM18505_IgG_NFKB | reviewing | 39 |
| hg18 | 946 | YDH_GM19099_IgG_NFKB | reviewing | 39 |
| hg18 | 947 | YDH_GM19193_IgG_NFKB | reviewing | 39 |
| hg18 | 950 | YDH_HUVEC_Pol2 | reviewing | 39 |
| hg18 | 951 | YDH_K562_ATF3 | reviewing | 39 |
| hg18 | 952 | YDH_K562_NELFe | reviewing | 39 |
| hg18 | 956 | YDH_GM12878_IgG_Control | reviewing | 39 |
| hg18 | 957 | YDH_GM12878_IgG_Pol2 | reviewing | 39 |
| hg18 | 959 | YDH_GM12892_IgG_Control | reviewing | 39 |
+------+------+--------------------------------+-----------+---------+
93 rows in set (0.00 sec)
/cluster/data/encode/pipeline/bin/encodeStatus.pl 633 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 634 released
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 952 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 956 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 957 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 959 released
select db,id,name,status,user_id from projects where user_id = 39 and db = 'hg18' and status = 'reviewing';
Empty set (0.00 sec)
2010-05-26 Yale PolyA
=====================
### Why isn't Yale RNA seq in the pushQ and dumped in Brian's lap???
1) Had waited a long tome for description. Have it now. Closed.
2) Mark all tracks as approved.
select db,id,name,status,user_id from projects where db = 'hg18' and status not in ('reviewing','released','revoked','new') and user_id = 39;
+------+-----+----------------------------+-----------+---------+
| db | id | name | status | user_id |
+------+-----+----------------------------+-----------+---------+
| hg18 | 276 | YHD_K562_PolyA_RNA | displayed | 39 |
| hg18 | 331 | YDH_RNAseq_RawSignal_Regen | displayed | 39 |
| hg18 | 539 | YDH_GM12878_ds_cDNA | displayed | 39 |
| hg18 | 540 | YDH_K562_IFNa30m_cDNA | displayed | 39 |
| hg18 | 541 | YDH_K562_IFNa6h_cDNA | displayed | 39 |
| hg18 | 542 | YDH_K562_IFNg30m_cDNA | displayed | 39 |
| hg18 | 543 | YDH_K562_IFNg6h_cDNA | displayed | 39 |
| hg18 | 788 | YDH_tagAlign_update_RNA | displayed | 39 |
+------+-----+----------------------------+-----------+---------+
8 rows in set (0.00 sec)
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 331 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 539 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 540 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 541 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 542 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 543 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 788 approved
3) Make release dir:
cd {downloads}/wgEncodeYaleRNAseq/
mkdir release1
cd release1/
ln ../*.gz .
cd ..
# edit preamble.html
# verify that mdb is complete: nope...
mdbUpdate hg18 fileDb.ra
mdbUpdate hg18 yaleRna.txt # from trackDb
encodeDownloadsPage.pl -mdb=metaDb_tdreszer -db=hg18 mdb.html
# okay now
mdbPrint hg18 -vars="composite=wgEncodeYaleRNAseq" > wgEncodeYaleRNAseq.ra
cvs ci
encodeDownloadsPage.pl -mdb=metaDb -db=hg18 -checksum index.html
4) Put pushQ together:
mdbPrint hg18 -vars="composite=wgEncodeYaleRNAseq objType=table" | grep metaObj
metaObject wgEncodeYaleRnaSeqPolyaRel2RawSignalK562
metaObject wgEncodeYaleRnaSeqPolyaSignalGm12878
metaObject wgEncodeYaleRnaSeqPolyaSignalK562
metaObject wgEncodeYaleRnaSeqPolyaSignalK562Ifna30m
metaObject wgEncodeYaleRnaSeqPolyaSignalK562Ifna6h
metaObject wgEncodeYaleRnaSeqPolyaSignalK562Ifng30m
metaObject wgEncodeYaleRnaSeqPolyaSignalK562Ifng6h
# remove the old and unneeded wgEncodeYaleRnaSeqPolyaRel2RawSignalK562
/cluster/data/encode/pipeline/bin/encodeStatus.pl 276 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 331 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 539 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 540 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 541 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 542 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 543 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 788 reviewing
select db,id,name,status,user_id from projects where db = 'hg18' and status not in ('reviewing','released','revoked','new') and user_id = 39;
Empty set (0.00 sec)
2011-01-03 For some reason subId=193 marked as loaded but is actually released.
===================================================
193 shows every sign of being released. I have verified that the data is on RR (hg18) and see that the submission was moved to "released" on 2009-03-16.
I show no record of its status being changed since, either in the status logs or the makeDb/doc file. I will change its status back to released.
update projects set status = released where id = 193;
2011-03-16 Load those ancient submissions into hg18
===================================================
Change Encode.pm to accept hg18
1182,1183,1184,1185,1186
select id,name,status from projects where id in (1182,1183,1184,1185,1186);
+------+--------------------+-----------+
| id | name | status |
+------+--------------------+-----------+
| 1182 | SYDH_GM12878_Max | hold hg18 | V3 - Includes previously missing sequence data
| 1183 | SYDH_GM12878_Pol2 | hold hg18 | V3 - Includes previously missing sequence data
| 1184 | SYDH_GM12878_c_Fos | hold hg18 | V3 - Includes previously missing sequence data
| 1185 | SYDH_GM12878_c_Jun | hold hg18 | new
| 1186 | SYDH_GM12878_c_Myc | hold hg18 | new
+------+--------------------+-----------+
update projects set status = "validate failed" where id in (1182,1183,1184,1185,1186);
# "validate failed" will allow re-"validate" from the pipeline
# edited all the DAFs to bring them to v2.0 standard.
# With a little wrenching, all were loaded
# Rename tables to hg18 standards
rename table wgEncodeYaleChIPseqGm12878CfosStdSigV3 to wgEncodeYaleChIPseqSignalGm12878CfosV3;
rename table wgEncodeYaleChIPseqGm12878CfosStdPkV3 to wgEncodeYaleChIPseqPeaksGm12878CfosV3;
rename table wgEncodeYaleChIPseqGm12878CmycStdSig to wgEncodeYaleChIPseqSignalGm12878Cmyc;
rename table wgEncodeYaleChIPseqGm12878CmycStdPk to wgEncodeYaleChIPseqPeaksGm12878Cmyc;
rename table wgEncodeYaleChIPseqGm12878MaxStdSigV3 to wgEncodeYaleChIPseqSignalGm12878MaxV3;
rename table wgEncodeYaleChIPseqGm12878MaxStdPkV3 to wgEncodeYaleChIPseqPeaksGm12878MaxV3;
rename table wgEncodeYaleChIPseqGm12878Pol2StdSigV3 to wgEncodeYaleChIPseqSignalGm12878Pol2V3;
rename table wgEncodeYaleChIPseqGm12878Pol2StdPkV3 to wgEncodeYaleChIPseqPeaksGm12878Pol2V3;
rename table wgEncodeYaleChIPseqGm12878CjunStdSig to wgEncodeYaleChIPseqSignalGm12878Cjun;
rename table wgEncodeYaleChIPseqGm12878CjunStdPk to wgEncodeYaleChIPseqPeaksGm12878Cjun;
# rename files to hg18 standards
cd {downloadsHg18}/wgEncodeYaleChIPseq
mv wgEncodeYaleChIPseqGm12878CfosStdAlnRep1V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878CfosV3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878CfosStdAlnRep2V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878CfosV3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878CfosStdSigV3.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878CfosV3.bedGraph4.gz
mv wgEncodeYaleChIPseqGm12878CfosStdPkV3.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878CfosV3.narrowPeak.gz
mv wgEncodeYaleChIPseqGm12878CfosStdRawDataRep1V3.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878CfosV3.fastq.gz
mv wgEncodeYaleChIPseqGm12878CfosStdRawDataRep2V3.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878CfosV3.fastq.gz
mv wgEncodeYaleChIPseqGm12878CmycStdAlnRep1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cmyc.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878CmycStdAlnRep2.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cmyc.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878CmycStdSig.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878Cmyc.bedGraph4.gz
mv wgEncodeYaleChIPseqGm12878CmycStdPk.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Cmyc.narrowPeak.gz
mv wgEncodeYaleChIPseqGm12878CmycStdRawDataRep1.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878Cmyc.fastq.gz
mv wgEncodeYaleChIPseqGm12878CmycStdRawDataRep2.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878Cmyc.fastq.gz
mv wgEncodeYaleChIPseqGm12878MaxStdAlnRep1V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878MaxV3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878MaxStdAlnRep2V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878MaxV3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878MaxStdSigV3.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878MaxV3.bedGraph4.gz
mv wgEncodeYaleChIPseqGm12878MaxStdPkV3.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878MaxV3.narrowPeak.gz
mv wgEncodeYaleChIPseqGm12878MaxStdRawDataRep1V3.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878MaxV3.fastq.gz
mv wgEncodeYaleChIPseqGm12878MaxStdRawDataRep2V3.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878MaxV3.fastq.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdAlnRep1V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2V3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdAlnRep2V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2V3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdAlnRep3V3.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep3Gm12878Pol2V3.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdSigV3.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878Pol2V3.bedGraph4.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdPkV3.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V3.narrowPeak.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdRawDataRep1V3.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878Pol2V3.fastq.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdRawDataRep2V3.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878Pol2V3.fastq.gz
mv wgEncodeYaleChIPseqGm12878Pol2StdRawDataRep3V3.fastq.gz wgEncodeYaleChIPseqRawDataRep3Gm12878Pol2V3.fastq.gz
mv wgEncodeYaleChIPseqGm12878CjunStdAlnRep1.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cjun.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878CjunStdAlnRep2.tagAlign.gz wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cjun.tagAlign.gz
mv wgEncodeYaleChIPseqGm12878CjunStdSig.bedGraph4.gz wgEncodeYaleChIPseqSignalGm12878Cjun.bedGraph4.gz
mv wgEncodeYaleChIPseqGm12878CjunStdPk.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Cjun.narrowPeak.gz
mv wgEncodeYaleChIPseqGm12878CjunStdRawDataRep1.fastq.gz wgEncodeYaleChIPseqRawDataRep1Gm12878Cjun.fastq.gz
mv wgEncodeYaleChIPseqGm12878CjunStdRawDataRep2.fastq.gz wgEncodeYaleChIPseqRawDataRep2Gm12878Cjun.fastq.gz
# edit mdb.txt for each and trackDb.ra for each
# load the metadata
mdbUpdate hg18 1182/out/mdb.txt
Read 6 metadata objects from hg18
Affected 128 row(s) in hg18.metaDb_tdreszer
mdbUpdate hg18 1183/out/mdb.txt
Read 8 metadata objects from hg18
Affected 170 row(s) in hg18.metaDb_tdreszer
mdbUpdate hg18 1184/out/mdb.txt
Read 6 metadata objects from hg18
Affected 128 row(s) in hg18.metaDb_tdreszer
mdbUpdate hg18 1185/out/mdb.txt
Read 6 metadata objects from hg18
Affected 116 row(s) in hg18.metaDb_tdreszer
mdbUpdate hg18 1186/out/mdb.txt
Read 6 metadata objects from hg18
Affected 116 row(s) in hg18.metaDb_tdreszer
cd {mdb18}
mdbPrint hg18 -composite=wgEncodeYaleChIPseq > wgEncodeYaleChIPseq.ra
# set up trackDb
cd ../../ {tdb/hg19}
e wgEncodeYaleChIPseq.new.ra
gold wgEncodeYaleChIPseq.new.ra # Minimum changes!
git up, add, ci push
make DBS=hg18
# update download dir
cd {downHg18}/wgEncodeYaleChIPseq
encodeDownloadsPage.pl -db=hg18 index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1182 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1183 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1184 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1185 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1186 displayed
List of tables:
wgEncodeYaleChIPseqSignalGm12878MaxV3 (replaces wgEncodeYaleChIPseqRel2SignalGm12878Max )
wgEncodeYaleChIPseqPeaksGm12878MaxV3 (replaces wgEncodeYaleChIPseqPeaksGm12878MaxV2 )
wgEncodeYaleChIPseqSignalGm12878Pol2V3 (replaces wgEncodeYaleChIPseqRel2SignalGm12878Pol2)
wgEncodeYaleChIPseqPeaksGm12878Pol2V3 (replaces wgEncodeYaleChIPseqPeaksGm12878Pol2V2 )
wgEncodeYaleChIPseqSignalGm12878CfosV3 (replaces wgEncodeYaleChIPseqRel2SignalGm12878Cfos)
wgEncodeYaleChIPseqPeaksGm12878CfosV3 (replaces wgEncodeYaleChIPseqPeaksGm12878CfosV2 )
wgEncodeYaleChIPseqSignalGm12878Cjun
wgEncodeYaleChIPseqPeaksGm12878Cjun
wgEncodeYaleChIPseqSignalGm12878Cmyc
wgEncodeYaleChIPseqPeaksGm12878Cmyc
List of files:
wgEncodeYaleChIPseqAlignmentsRep1Gm12878MaxV3.tagAlign.gz (replaces wgEncodeYaleChIPseqAlignmentsRep1Gm12878MaxV2.tagAlign.gz )
wgEncodeYaleChIPseqAlignmentsRep2Gm12878MaxV3.tagAlign.gz (replaces wgEncodeYaleChIPseqAlignmentsRep2Gm12878MaxV2.tagAlign.gz )
wgEncodeYaleChIPseqSignalGm12878MaxV3.bedGraph4.gz (replaces wgEncodeYaleChIPseqRel2SignalGm12878Max.bedGraph4.gz )
wgEncodeYaleChIPseqPeaksGm12878MaxV3.narrowPeak.gz (replaces wgEncodeYaleChIPseqPeaksGm12878MaxV2.narrowPeak.gz )
wgEncodeYaleChIPseqRawDataRep1Gm12878MaxV3.fastq.gz (replaces wgEncodeYaleChIPseqRawDataRep1Gm12878Max.fastq.gz )
wgEncodeYaleChIPseqRawDataRep2Gm12878MaxV3.fastq.gz (replaces wgEncodeYaleChIPseqRawDataRep2Gm12878Max.fastq.gz )
wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2V3.tagAlign.gz (replaces wgEncodeYaleChIPseqAlignmentsRep1Gm12878Pol2V2.tagAlign.gz)
wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2V3.tagAlign.gz (replaces wgEncodeYaleChIPseqAlignmentsRep2Gm12878Pol2V2.tagAlign.gz)
wgEncodeYaleChIPseqAlignmentsRep3Gm12878Pol2V3.tagAlign.gz (replaces - nothing - )
wgEncodeYaleChIPseqSignalGm12878Pol2V3.bedGraph4.gz (replaces wgEncodeYaleChIPseqRel2SignalGm12878Pol2.bedGraph4.gz )
wgEncodeYaleChIPseqPeaksGm12878Pol2V3.narrowPeak.gz (replaces wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz )
wgEncodeYaleChIPseqRawDataRep1Gm12878Pol2V3.fastq.gz (replaces wgEncodeYaleChIPseqRawDataRep1Gm12878Pol2.fastq.gz )
wgEncodeYaleChIPseqRawDataRep2Gm12878Pol2V3.fastq.gz (replaces wgEncodeYaleChIPseqRawDataRep2Gm12878Pol2.fastq.gz )
wgEncodeYaleChIPseqRawDataRep3Gm12878Pol2V3.fastq.gz (replaces - nothing - )
wgEncodeYaleChIPseqAlignmentsRep1Gm12878CfosV3.tagAlign.gz (replaces wgEncodeYaleChIPseqAlignmentsRep1Gm12878CfosV2.tagAlign.gz)
wgEncodeYaleChIPseqAlignmentsRep2Gm12878CfosV3.tagAlign.gz (replaces wgEncodeYaleChIPseqAlignmentsRep2Gm12878CfosV2.tagAlign.gz)
- nothing - (replaces wgEncodeYaleChIPseqAlignmentsRep3Gm12878CfosV2.tagAlign.gz)
wgEncodeYaleChIPseqSignalGm12878CfosV3.bedGraph4.gz (replaces wgEncodeYaleChIPseqRel2SignalGm12878Cfos.bedGraph4.gz )
wgEncodeYaleChIPseqPeaksGm12878CfosV3.narrowPeak.gz (replaces wgEncodeYaleChIPseqPeaksGm12878CfosV2.narrowPeak.gz )
wgEncodeYaleChIPseqRawDataRep1Gm12878CfosV3.fastq.gz (replaces wgEncodeYaleChIPseqRawDataRep1Gm12878Cfos.fastq.gz )
wgEncodeYaleChIPseqRawDataRep2Gm12878CfosV3.fastq.gz (replaces wgEncodeYaleChIPseqRawDataRep2Gm12878Cfos.fastq.gz )
- nothing - (replaces wgEncodeYaleChIPseqRawDataRep3Gm12878Cfos.fastq.gz )
wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cjun.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cjun.tagAlign.gz
wgEncodeYaleChIPseqSignalGm12878Cjun.bedGraph4.gz
wgEncodeYaleChIPseqPeaksGm12878Cjun.narrowPeak.gz
wgEncodeYaleChIPseqRawDataRep1Gm12878Cjun.fastq.gz
wgEncodeYaleChIPseqRawDataRep2Gm12878Cjun.fastq.gz
wgEncodeYaleChIPseqAlignmentsRep1Gm12878Cmyc.tagAlign.gz
wgEncodeYaleChIPseqAlignmentsRep2Gm12878Cmyc.tagAlign.gz
wgEncodeYaleChIPseqSignalGm12878Cmyc.bedGraph4.gz
wgEncodeYaleChIPseqPeaksGm12878Cmyc.narrowPeak.gz
wgEncodeYaleChIPseqRawDataRep1Gm12878Cmyc.fastq.gz
wgEncodeYaleChIPseqRawDataRep2Gm12878Cmyc.fastq.gz
### Clean up sigs that overrun chrom:
hg18.wgEncodeYaleChIPseqSignalGm12878CfosV3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878CfosV3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cjun has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Cmyc has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878MaxV3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878MaxV3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878MaxV3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878MaxV3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Pol2V3 has 1 records with end > chromSize.
hg18.wgEncodeYaleChIPseqSignalGm12878Pol2V3 has 1 records with end > chromSize.
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr8" and chromEnd > 146274826;
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr15" and chromEnd > 100338915; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr18" and chromEnd > 76117153; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqSignalGm12878CfosV3 where chrom = "chr21" and chromEnd > 46944323;
update wgEncodeYaleChIPseqSignalGm12878CfosV3 set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqSignalGm12878CfosV3 set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr7" and chromEnd > 158821424; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr8" and chromEnd > 146274826; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr10" and chromEnd > 135374737; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr15" and chromEnd > 100338915; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cjun where chrom = "chr21" and chromEnd > 46944323; #1
update wgEncodeYaleChIPseqSignalGm12878Cjun set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalGm12878Cjun set chromEnd = 146274826 where chrom = "chr8" and chromEnd > 146274826;
update wgEncodeYaleChIPseqSignalGm12878Cjun set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalGm12878Cjun set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqSignalGm12878Cjun set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr7" and chromEnd > 158821424; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr8" and chromEnd > 146274826;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr10" and chromEnd > 135374737; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr15" and chromEnd > 100338915;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr18" and chromEnd > 76117153; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Cmyc where chrom = "chr21" and chromEnd > 46944323; #1
update wgEncodeYaleChIPseqSignalGm12878Cmyc set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalGm12878Cmyc set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalGm12878Cmyc set chromEnd = 76117153 where chrom = "chr18" and chromEnd > 76117153 ;
update wgEncodeYaleChIPseqSignalGm12878Cmyc set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr7" and chromEnd > 158821424; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr8" and chromEnd > 146274826;
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr10" and chromEnd > 135374737; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr15" and chromEnd > 100338915; #1
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqSignalGm12878MaxV3 where chrom = "chr21" and chromEnd > 46944323; #1
update wgEncodeYaleChIPseqSignalGm12878MaxV3 set chromEnd = 158821424 where chrom = "chr7" and chromEnd > 158821424;
update wgEncodeYaleChIPseqSignalGm12878MaxV3 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalGm12878MaxV3 set chromEnd = 100338915 where chrom = "chr15" and chromEnd > 100338915;
update wgEncodeYaleChIPseqSignalGm12878MaxV3 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr7" and chromEnd > 158821424;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr8" and chromEnd > 146274826;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr10" and chromEnd > 135374737;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr15" and chromEnd > 100338915;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr18" and chromEnd > 76117153;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr20" and chromEnd > 62435964;
select count(*) from wgEncodeYaleChIPseqSignalGm12878Pol2V3 where chrom = "chr21" and chromEnd > 46944323;
update wgEncodeYaleChIPseqSignalGm12878Pol2V3 set chromEnd = 135374737 where chrom = "chr10" and chromEnd > 135374737;
update wgEncodeYaleChIPseqSignalGm12878Pol2V3 set chromEnd = 46944323 where chrom = "chr21" and chromEnd > 46944323 ;