# convert Mac => Unix: tr '\r' '\n' < StanfordChip-FOXP2.DDF.original > StanfordChip-FOXP2.DDF Q) discrepancies b/n DDF and data directory? awk '{print $1}' StanfordChip-FOXP2.DDF > 1.txt remove first line ls data | awk '{print $1}' | sort > 2.txt diff 1.txt 2.txt 0a1 > FoxP2_PFSK1_SL102_hg18.TagAlign 6d6 < FoxP2_SK-N-MC_SL102_hg18.TagAlign Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/Encode.pm line 275. Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/Encode.pm line 275. Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/Encode.pm line 304. add "data/" prefix for all files change "PSFK-1" to "PFSK-1" in DDF Format of narrowPeak file FoxP2_PFSK1_SL13_peakcalls.narrowPeak is invalid (missing many columns). grep '^newcontam' data/FoxP2_PFSK1_SL16_hg18.TagAlign data/FoxP2_PFSK1_SL16_hg18.TagAlign data/FoxP2_SK-N-MC_SL102_hg18.TagAlign Q) Figure out what are the weird chrom names? perl -e 'while(<>) {if(/^(\S+)/) {$hash{$1}++;}} print join("\n", sort keys %hash) . "\n";' FoxP2_SK-N-MC_SL102_hg18.TagAlign > uniq.txt & found 2 odd chrom names: humRibosomal.fasta newcontam egrep -v '^(newcontam|humRibosomal\.fasta)' FoxP2_SK-N-MC_SL102_hg18.TagAlign.original > FoxP2_SK-N-MC_SL102_hg18.TagAlign egrep -v '^(newcontam|humRibosomal\.fasta)' FoxP2_PFSK1_SL16_hg18.TagAlign.original > FoxP2_PFSK1_SL16_hg18.TagAlign Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 742. Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 767. Use of uninitialized value in addition (+) at /cluster/bin/scripts/doEncodeValidate.pl line 769. Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776. Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776. View: RawSignal Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 742. Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 767. Use of uninitialized value in addition (+) at /cluster/bin/scripts/doEncodeValidate.pl line 769. Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776. Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776. caused by MS-DOS text files (ugh). Q) How big are the files? One of the control tagAlign files: wc -l data/FoxP2_PFSK1_SL16_hg18.TagAlign.original 23,550,618 One of the experimental files: wc -l FoxP2_SK-N-MC_SL144_hg18.TagAlign 13,411,341 Rename the project Rami created: hgsql encpipeline_prod update projects set name = 'HudsonAlpha PFSK-1/SK-N-MC Control' where id = 6; hgLoadBed hg18 HAMethylSeq ~/tmp/methyl.bed -tmpDir=/data/tmp -bedGraph=4 hgLoadBed hg18 HAMethylSeq ~/tmp/HCT116_hpaII.txt.BED -tmpDir=/data/tmp -bedGraph=4 2009-02-10: Fixed various errors in HudsonAlpha_MethylSeq_Feb0909.DDF (add/subtract tabs etc.) /cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/204 >& validate_error & Orange = methylated; blue = non-methylated Hypomethylation in HAL, and fetus and BG02ES (but no gene nearby): chr6:31,247,115-31,267,634 Hypomethylation in human adult liver, and fetus: chr12:112,685,995-112,696,308 Hypomethylation in human adult liver, and fetus: chr17:7,584,398-7,586,905 Hypermethylation only in a cancer cell: chr17:7,548,069-7,550,576 chr12:112,375,893-112,403,444 (LHX5) Hypermethylation only in late fetus and adult: chr12:120,130,554-120,135,393 chr1:219,118,454-219,126,339 (HLX, but not near promoter) /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/204 > upload_error 2>&1 & 2009-02 round: 251, 259-262 TODO: /hive/groups/encode/dcc/pipeline/encpipeline_prod/251 - figure out how to deal with control; e.g.: exp_data/Methylseq_GM12878_R1_hpa_1pcr.TagAlign Alignments GM12878 1 exp_data/Methylseq_GM12878_R1_msp_1pcr.TagAlign Alignments GM12878 1 ######################################################################################################### # Deal with loading ftp data after that fact # 2009 ######################################################################################################### Larry, I'm currenly sending our fastq files for most of our ChIP-Seq submissions so far: HudsonAlphaChip_Bg_GM12878_K562 HudsonAlphaChip_RNAPol2_GM12878_K562 HudsonAlphaChip_GABP_GM12878_K562 HudsonAlphaChip_NRSF_GM12878_K562 HudsonAlphaChip_SRF_GM12878_K562 HudsonAlphaChip_TAF250_GM12878_Dec08 HudsonAlphaChip_TAF250_K562_Dec08 Each of the above will be represented by a tar.gz names FASTQ_. Inside each tar.gz are .fasq files for each of the experiments (uniquely marked by the Library Id - ex: ..._SL242_...fastq). D FASTQ_HudsonAlphaChip_Bg_GM12878_K562.tar.gz D FASTQ_HudsonAlphaChip_GABP_GM12878_K562.tar.gz D FASTQ_HudsonAlphaChip_NRSF_GM12878_K562.tar.gz D FASTQ_HudsonAlphaChip_RNAPol2_GM12878_K562.tar.gz D FASTQ_HudsonAlphaChip_SRF_GM12878_K562.tar.gz W FASTQ_HudsonAlphaChip_TAF250_GM12878_Dec08.tar.gz - only 1 experiment? Gm12878/TafII? W FASTQ_HudsonAlphaChip_TAF250_K562_Dec08.tar.gz Each of the above will be represented by a tar.gz names FASTQ_. Inside each tar.gz are .fasq files for each of the experiments (uniquely marked by the Library Id - ex: ..._SL242_...fastq). "Bg" = control/input tar tzvf FASTQ_HudsonAlphaChip_NRSF_GM12878_K562.tar.gz drwxr-xr-x encode/staff 0 2009-01-14 14:56:16 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/ -rw-r--r-- encode/staff 193832511 2009-01-14 14:26:06 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30DMJAAXX_SL202_s_1_sequence.txt.fastq -rw-r--r-- encode/staff 130633836 2009-01-14 14:32:00 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_1_sequence.txt.fastq -rw-r--r-- encode/staff 338440635 2009-01-14 14:32:10 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_2_sequence.txt.fastq -rw-r--r-- encode/staff 277341720 2009-01-14 14:32:18 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_3_sequence.txt.fastq -rw-r--r-- encode/staff 561864878 2009-01-14 14:32:34 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_8_sequence.txt.fastq -rw-r--r-- encode/staff 187817403 2009-01-14 14:26:11 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ET2AAXX_SL202_s_2_sequence.txt.fastq -rw-r--r-- encode/staff 291247386 2009-01-14 14:32:43 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ET2AAXX_SL204_s_8_sequence.txt.fastq -rw-r--r-- encode/staff 715598490 2009-01-14 14:33:04 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30GJ8AAXX_SL221_s_4_sequence.txt.fastq -rw-r--r-- encode/staff 196632239 2009-01-14 14:33:09 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204GV_SL204_s_1_sequence.txt.fastq -rw-r--r-- encode/staff 208102467 2009-01-14 14:33:15 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204GV_SL204_s_2_sequence.txt.fastq -rw-r--r-- encode/staff 253398035 2009-01-14 14:33:23 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204GV_SL204_s_3_sequence.txt.fastq -rw-r--r-- encode/staff 356976207 2009-01-14 14:26:22 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_1_sequence.txt.fastq -rw-r--r-- encode/staff 379577169 2009-01-14 14:26:32 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_2_sequence.txt.fastq -rw-r--r-- encode/staff 395860545 2009-01-14 14:26:44 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_3_sequence.txt.fastq -rw-r--r-- encode/staff 395647171 2009-01-14 14:26:55 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_4_sequence.txt.fastq -rw-r--r-- encode/staff 361962255 2009-01-14 14:27:05 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209TN_SL202_s_5_sequence.txt.fastq -rw-r--r-- encode/staff 343422718 2009-01-14 14:33:33 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209TN_SL204_s_7_sequence.txt.fastq -rw-r--r-- encode/staff 302635377 2009-01-14 14:33:41 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL221_s_1_sequence.txt.fastq -rw-r--r-- encode/staff 424945463 2009-01-14 14:33:54 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL221_s_2_sequence.txt.fastq -rw-r--r-- encode/staff 333914738 2009-01-14 14:34:03 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL222_s_3_sequence.txt.fastq -rw-r--r-- encode/staff 344272962 2009-01-14 14:34:13 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL222_s_4_sequence.txt.fastq -rw-r--r-- encode/staff 486213829 2009-01-14 14:34:27 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20AJD_SL221_s_4_sequence.txt.fastq -rw-r--r-- encode/staff 469495268 2009-01-14 14:34:41 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20AJD_SL222_s_5_sequence.txt.fastq -rw-r--r-- encode/staff 557509406 2009-01-14 14:34:56 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL204_s_3_sequence.txt.fastq -rw-r--r-- encode/staff 562488011 2009-01-14 14:35:12 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL204_s_4_sequence.txt.fastq -rw-r--r-- encode/staff 589184958 2009-01-14 14:35:29 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL221_s_5_sequence.txt.fastq -rw-r--r-- encode/staff 597901196 2009-01-14 14:35:47 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL221_s_6_sequence.txt.fastq -rw-r--r-- encode/staff 512389254 2009-01-14 14:36:02 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL222_s_7_sequence.txt.fastq -rw-r--r-- encode/staff 540333106 2009-01-14 14:36:17 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL222_s_8_sequence.txt.fastq find . -type f -exec cat {} \; | gzip -c > /cluster/data/encode/pipeline/downloads/wgEncodeHudsonalphaChipSeq/wgEncodeHudsonalphaChipSeqRawSignalRep1Gm12878Control.gz Sanity checking: zcat /hive/groups/encode/dcc/analysis/ftp/pipeline/wgEncodeHudsonalphaChipSeq/wgEncodeHudsonalphaChipSeqAlignmentsRep1Gm12878Control.tagAlign.gz | wc -l 14164649 - 14 million replicate2: 16222442 - 16 million cd /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch/FASTQ_HudsonAlphaChip_Bg_GM12878_K562 egrep '^@' FC30P52AAXX_SL233_s_7_sequence.txt.fastq | wc -l 5,191,814 5,191,814 * 30 = 155,754,420 That's 155 million reads for both replicates? They only used 1/10 of the reads? filename(s) cell antibody replicate control cat FC20AME_SL217_s_4_sequence.txt.fastq FC20ATK_SL217_s_1_sequence.txt.fastq FC20ATK_SL217_s_2_sequence.txt.fastq FC20ATK_SL217_s_3_sequence.txt.fastq FC20ATK_SL217_s_4_sequence.txt.fastq GM12878 . 1 true cat 30EMPAAXX_SL218_s_1_sequence.txt.fastq FC20AME_SL218_s_5_sequence.txt.fastq FC20ATK_SL218_s_5_sequence.txt.fastq FC20ATK_SL218_s_6_sequence.txt.fastq FC20ATK_SL218_s_7_sequence.txt.fastq FC20ATK_SL218_s_8_sequence.txt.fastq GM12878 . 2 true cat 303praaxx_SL233_s_4_sequence.txt.fastq 30DCTAAXX_SL233_s_1_sequence.txt.fastq 30DKKAAXX_SL233_s_5_sequence.txt.fastq 30DLBAAXX_SL233_s_1_sequence.txt.fastq 30EMPAAXX_SL233_s_2_sequence.txt.fastq 30G4WAAXX_SL233_s_3_sequence.txt.fastq 30P07AAXX_SL233_s_4_sequence.txt.fastq FC209VY_SL233_s_4_sequence.txt.fastq FC20E3HAAXX_SL233_s_4_sequence.txt.fastq FC30P52AAXX_SL233_s_3_sequence.txt.fastq FC30P52AAXX_SL233_s_7_sequence.txt.fastq K562 . 1 true cat 303praaxx_SL234_s_5_sequence.txt.fastq 30DCTAAXX_SL234_s_2_sequence.txt.fastq 30EFCAAXX_SL234_s_1_sequence.txt.fastq 30EFCAAXX_SL234_s_2_sequence.txt.fastq 30EMPAAXX_SL234_s_3_sequence.txt.fastq 30G4WAAXX_SL234_s_4_sequence.txt.fastq FC209VY_SL234_s_5_sequence.txt.fastq FC20E3HAAXX_SL234_s_5_sequence.txt.fastq K562 . 2 true cd /hive/groups/encode/dcc/analysis/ftp/pipeline/wgEncodeHudsonalphaChipSeq zcat *fastq.gz | wc -l 499097056 cd /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch/FASTQ_HudsonAlphaChip_Bg_GM12878_K562 cat *.fastq | wc -l 499097056 they match (good!) touch -r wgEncodeHudsonalphaChipSeqAlignmentsPfsk1Control.tagAlign.gz *fastq* # figure out which files are missing ls -lt *tagAlign.gz* | perl -ne 's/(RawData|Alignments)//g; if(/(\S+?)\./) { print "$1\n"; }' | sort > tagAlign.txt ls -lt *fastq.gz* | perl -ne 's/(RawData|Alignments)//g; if(/(\S+?)\./) { print "$1\n"; }' | sort > fastq.txt diff tagAlign.txt fastq.txt Q) How do I make sure that Rami didn't screw up and give us non-matching fastq's? pushd /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeHudsonalphaChipSeq/ ~/tmp/faSanityCheck.pl *tagAlign.gz Couldn't find GAAGTAGTGAGACAGTGAGTTGGAT from wgEncodeHudsonalphaChipSeqAlignmentsRep1K562Tafii.tagAlign.gz in wgEncodeHudsonalphaChipSeqRawDataRep1K562Tafii.fastq.gz Confirmed by re-running the command. /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch/FASTQ_HudsonAlphaChip_TAF250_K562_Dec08 grep GAAGTAGTGAGACAGTGAGTTGGAT *.fastq finds nothing (another confirmation). Is this a TAF-II vs. TAF250 issue? How about in Yale data? pushd /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq Couldn't find TTTATGTTTCTTTTTGTCTTCTCTCTTT from wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz in wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz With reverse logic: Couldn't find TACTCTAATCCTTACAGAAAAAAAAAGA from wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz in wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz # that is line 38 of wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz chr7 49295084 49295112 TCTTTTTTTTTCTGTAAGGATTAGAGTA 1000 - # and line 146 of wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz Therefore, they do NOT put the reverse strand in the tagAlign file. zcat wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz | more chr18 28418426 28418454 CAGTCGATTTCCATTATTGAAGTTAGAA 250 + chr1 81592198 81592226 GGCATGAATCTTTGAGAAGCGTAGCTTT 250 + chr6 165185914 165185942 CATTTGGATTTCCTGTTATAACAAAAAT 1000 + chr3 96059483 96059511 AAGGACTCCCTCTTCAATAATTGGTTCT 250 - I couldn't find line 4, AAGGACTCCCTCTTCAATAATTGGTTCT, its complement or complement reverse in wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz However, the first line of the tagAlign, CAGTCGATTTCCATTATTGAAGTTAGAA, is on line 2 of wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz zcat wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz | wc -l 55,835,940 / 4 = 13,958,985 zcat wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz | wc -l 11,543,712 zcat wgEncodeYaleChIPseqRawDataRep3Nb4Pol2.fastq.gz | wc -l 19443428 / 4 = 4,860,857 zcat wgEncodeYaleChIPseqAlignmentsRep3Nb4Pol2.tagAlign.gz | wc -l 4,330,530 So, they use almost all of their reads?!? That seems suspicious. And even more places (UTA): [larrym@hgwdev wgEncodeChromatinMap]$ ~/kent/src/hg/encode/encodeValidate/tagAlignSanityCheck.pl -reverse wgEncodeUtaChIPseqAlignmentsRep*tagAlign* Couldn't find the following sequences from wgEncodeUtaChIPseqAlignmentsRep3Gm12878Ctcf.tagAlign.gz in wgEncodeUtaChIPseqRawDataRep3Gm12878Ctcf.fastq.gz AAGCATGGTGGCATGCGCATGTGGTCCCAGANC But maybe that's b/c it's not reversed 2009-04-03 Rami uploaded PFSK-1 and SK-N-MC replicates 1 and 2 and control - cd /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch tar xzvf HudsonAlpha_PFSK-1_SK-N-MC_FOXP2_FASTQ.tar.gz cd PFSK-1_SK-N-MC_FOXP2_FASTQ ~/tmp/ramiDdf.pl < ~/tmp/fpsk.ddf generated wgEncodeHudsonalphaChipSeqRawDataRep2SknmcFoxp2.fastq.gz and wgEncodeHudsonalphaChipSeqRawDataRep2Pfsk1Foxp2.fastq.gz ~/kent/src/hg/encode/encodeValidate/tagAlignSanityCheck.pl *Rep2SknmcFoxp2.tagAlign.gz *Rep2Pfsk1Foxp2.tagAlign.gz wgEncodeHudsonalphaChipSeqAlignmentsRep2SknmcFoxp2.tagAlign.gz is ok Couldn't find the following sequences from wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Foxp2.tagAlign.gz in wgEncodeHudsonalphaChipSeqRawDataRep2Pfsk1Foxp2.fastq.gz CATTTTACAGATGGAGAAACAGATT ACTTACAGTCATGGCACAAGGGGAA CTCATGTCAACGTTAAAAATGCTGT GAACCAGGTGTGAACTGGTGTCTAG AGTCCTGAGAATTCTACATCTCACG TTTGTAACGACAGGGTCTTGCTATG (6 out of 10). Still missing replicate 1 for FOXP2 in PFSK-1 and SK-N-MC! ######################################################################################################### # Put whatever we can into the pushQ # 2009-04-23 ######################################################################################################### pushQ items that are ready: releaseLogUrl = http://genome.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeHudsonalphaChipseq # this are still missing fastqs (PFSK-1, SK-N-MC data) 6 -> 004635 7 -> 004636 # these are ready 52 -> 004636 51 -> 004637 67 -> 004638 70 -> 004639 71 -> 004640 125 -> 004641 126 -> 004642 all seven have been consolidated into: 004636 2009-09-22 Tim is taking over! ============================== select id,name,status,user_id from projects where user_id = 8; +-----+----------------------------------------------------+-----------------+---------+ | id | name | status | user_id | +-----+----------------------------------------------------+-----------------+---------+ | 6 | HudsonAlpha PFSK-1/SK-N-MC Control | approved | 8 | | 7 | HudsonAlpha PFSK-1/SK-N-MC FOXP2 | approved | 8 | | 51 | HudsonAlphaChip_Bg_GM12878_K562 | released | 8 | | 52 | HudsonAlphaChip_RNAPol2_GM12878_K562 | released | 8 | | 67 | HudsonAlphaChip_GABP_GM12878_K562 | released | 8 | | 70 | HudsonAlphaChip_NRSF_GM12878_K562 | released | 8 | | 71 | HudsonAlphaChip_SRF_GM12878_K562 | released | 8 | | 103 | HudsonAlpha_Genotype_K562_GM12878_HepG2 | validate failed | 8 | | 125 | HudsonAlphaChip_TAF250_GM12878_Dec08 | released | 8 | | 126 | HudsonAlphaChip_TAF250_K562_Dec08 | released | 8 | | 204 | HudsonAlpha_Methyl_Seq_Feb0909 | approved | 8 | | 259 | HudsonAlpha_ChIPSeq_Sin3Ak-20_K562_GM12878_Feb2709 | displayed | 8 | | 260 | HudsonAlpha_ChIPSeq_Egr-1_K562_GM12878_Feb2709 | displayed | 8 | | 261 | HudsonAlpha_ChIPSeq_USF-1_K562_GM12878_Feb2709 | displayed | 8 | | 262 | HudsonAlpha_ChIPSeq_CONTROL_K562_GM12878_Feb2709 | displayed | 8 | | 268 | HudsonAlpha_ChIP-Seq-FEB09_FASTQ | loaded | 8 | | 387 | HudsonAlpha_MethylSeq_K562_GM12878_Mar09 | displayed | 8 | | 419 | HudsonAlpha_HepG2_Jul-09_FASTQ | validate failed | 8 | | 422 | HudsonAlpha_GM12878_Jul-09 | displayed | 8 | | 432 | HudsonAlpha_HepG2_Jul-09 | displayed | 8 | | 433 | HudsonAlpha_HeLa_Jul-09 | displayed | 8 | | 434 | HudsonAlpha_U87_Jul-09 | displayed | 8 | | 435 | HudsonAlpha_PANC1_Jul-09 | displayed | 8 | | 436 | HudsonAlpha_PFSK1_Jul-09 | displayed | 8 | | 437 | HudsonAlpha_BE2C_Jul-09 | displayed | 8 | | 438 | HudsonAlpha_HTB11_Jul-09 | displayed | 8 | +-----+----------------------------------------------------+-----------------+---------+ 26 rows in set (0.00 sec) Not to bad. Why 2 validate failed? It appears that: 1) no signals are provided. 2) We generate Raw Signals for ChIPseq 3) fastq are provided separately for ChIPseq. 4) Replicates go all the way up to the top: ChIPseq:peaks, MethylSeq:regions 5) Only Regions are displayed in MethylSeq 6) No Methyl27 submission. Track seems to be hand loaded. 7) Dir 103 is CNV which also seems to have been hand loaded and is owned by Brian.