### broadBernstein.txt wrangler notes for all submissions select id,name,status from projects where name like "Broad%"; +-----+--------------------------------------------+------------+ | id | name | status | +-----+--------------------------------------------+------------+ | 66 | Broad ChIPSeq K562 112008 | superceded | | 108 | Broad Raw Signal Regeneration | superceded | | 140 | Broad ChIPSeq GM12878 H3K4me3 010409 | released | | 141 | Broad ChIPSeq GM12878 H3K4me2 010408 | released | | 142 | Broad ChIPSeq GM12878 H3K4me1 010408 | released | | 143 | Broad ChIPSeq GM12878 H3K36me3 010408 | released | | 144 | Broad ChIPSeq GM12878 H3K27me3 010408 | released | | 145 | Broad ChIPSeq GM12878 H3K27ac 010408 | released | | 146 | Broad ChIPSeq GM12878 H3K9ac 010408 | released | | 147 | Broad ChIPSeq GM12878 H4K20me1 010409 | released | | 148 | Broad ChIPSeq GM12878 CTCF 010409 | released | | 149 | Broad ChIPSeq GM12878 WCE 010409 | released | | 150 | Broad ChIPSeq K562 H3K4me3 010409 | released | | 151 | Broad ChIPSeq K562 H3K4me2 010409 | released | | 152 | Broad ChIPSeq K562 H3K4me1 010409 | released | | 153 | Broad ChIPSeq K562 H3K27me3 010409 | released | | 154 | Broad ChIPSeq K562 H3K36me3 010409 | released | | 155 | Broad ChIPSeq K562 H3K9ac 010409 | released | | 156 | Broad ChIPSeq K562 H3K27ac 010409 | released | | 157 | Broad ChIPSeq K562 CTCF 010409 | released | | 158 | Broad ChIPSeq K562 H3K9me1 010409 | released | | 159 | Broad ChIPSeq K562 H4K20me1 010409 | released | | 160 | Broad ChIPSeq K562 Pol2 010409 | released | | 161 | Broad ChIPSeq K562 WCE 010409 | released | | 162 | Broad ChIPSeq HUVEC H3K4me3 010409 | released | | 163 | Broad ChIPSeq HUVEC H3K4me2 010409 | released | | 164 | Broad ChIPSeq HUVEC H3K4me1 010409 | released | | 165 | Broad ChIPSeq HUVEC H3K27me3 010409 | released | | 166 | Broad ChIPSeq HUVEC H3K36me3 010409 | released | | 167 | Broad ChIPSeq HUVEC H3K9ac 010409 | released | | 168 | Broad ChIPSeq HUVEC H3K27ac 010409 | released | | 169 | Broad ChIPSeq HUVEC H3K9me1 010409 | released | | 170 | Broad ChIPSeq HUVEC H4K20me1 010409 | released | | 171 | Broad ChIPSeq HUVEC CTCF 010409 | released | | 172 | Broad ChIPSeq HUVEC Pol2 010409 | released | | 173 | Broad ChIPSeq HUVEC WCE 010409 | released | | 174 | Broad ChIPSeq Keratinocyte H3K4me3 010409 | released | | 175 | Broad ChIPSeq Keratinocyte H3K4me2 010409 | released | | 176 | Broad ChIPSeq Keratinocyte H3K4me1 010409 | released | | 177 | Broad ChIPSeq Keratinocyte H3K27me3 010409 | released | | 178 | Broad ChIPSeq Keratinocyte H3K36me3 010409 | released | | 179 | Broad ChIPSeq Keratinocyte H3K9ac 010409 | released | | 180 | Broad ChIPSeq Keratinocyte H3K27ac 010409 | released | | 181 | Broad ChIPSeq Keratinocyte H3K9me1 | released | | 182 | Broad ChIPSeq Keratinocyte H4K20me1 010409 | released | | 183 | Broad ChIPSeq Keratinocyte CTCF 010409 | released | | 184 | Broad ChIPSeq Keratinocyte Pol2 010409 | released | | 185 | Broad ChIPSeq Keratinocyte WCE 010409 | released | +-----+--------------------------------------------+------------+ 48 rows in set (0.00 sec) Broad 11-20 =========== 1) cd 66;mv ../../ftp/prod/tarjei/Broad* . 2) tar -xzf Broad*.tgz tar -xzf BroadChipSeq_K562_H3K27ac_111908.tgz mv BroadChipSeq_K562_H3K27ac_111908.tgz 001_BroadChipSeq_K562_H3K27ac_111908.tgz tar;mv;tar;mv ... Everything expands to seq/tarjeiscratch/ENCODE/K562/data/ instead of data/ mv seq/tarjeiscratch/ENCODE/K562/data . 3) Validate /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 File 'data/Broad_Raw_K562_H3K4me3_rep1_chr*.fastq' does not exist (possibly bad glob?) Fix DDF Invalid tagAlign file; line 1 in file 'data/Broad_Raw_K562_H3K4me3_rep1_chr1.bed' is invalid: line: chr1 236781326 236781378 SL-XBE_3_FC30CLLAAXX:6:7:148:1114 GACAATTTATGGAGAAATATTAATCACAGTGCCTCATTAATTAATTCATTT 1000 + [validateTagAlign] chr1 236781326 236781378 SL-XBE_3_FC30CLLAAXX:6:7:148:1114 GACAATTTATGGAGAAATATTAATCACAGTGCCTCATTAATTAATTCATTT 1000 + mv Broad_Raw_K562_WCE_rep2_chrX.bed old awk '{printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$5,$6,$7;}' Broad_Raw_K562_WCE_rep2_chrX.bed > Broad_Raw_K562_WCE_rep2_chrX.bed.test cd data mkdir old mv *.bed old/ cd old for file in *.bed do echo Fixing $file... awk '{printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$5,$6,$7;}' $file > ../$file done File 'data/Broad_K562_H3K4me3_chr1.wig' failed wiggle validation: Found start=0 at line 1, the first chrom position is 1, not 0 cd data mkdir old mv *.wig old/ cd old for file in *.wig do echo Fixing $file... cat $file | sed s/"start=0"/"start=1"/g > ../$file done cd data grep fixedStep Broad_K562_H3K4me3_chr1.wig grep -v fixedStep Broad_K562_H3K4me3_chr1.wig > new/Broad_K562_H3K4me3_chr1.wig Broad 11-26 =========== /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 & Failed.. Added medianFragmentLength 225 removed controls /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/66 > upload_error 2>&1 & Broad 11-30 Control =================== edit BroadChipSeq.ddf to BroadChipSeqJustInput.DDF alter doEncodeValidate.pl to ignore required on control or input. /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/66 > upload_error 2>&1 & | wgEncodeBroadChipSeqRawSignalRep1K562Control | | wgEncodeBroadChipSeqRawSignalRep1K562Ctcf | | wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac | | wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac | | wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1 | | wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1 | | wgEncodeBroadChipSeqRawSignalRep1K562Pol2b | | wgEncodeBroadChipSeqRawSignalRep2K562Control | | wgEncodeBroadChipSeqRawSignalRep2K562Ctcf | | wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac | | wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac | | wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1 | | wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1 | | wgEncodeBroadChipSeqRawSignalRep2K562Pol2b | data/Broad_Raw_K562_H3K4me3_rep1_chr*.bed Alignments K562 H3K4me3 1 data/Broad_Raw_K562_H3K4me3_rep2_chr*.bed Alignments K562 H3K4me3 2 data/Broad_Raw_K562_H3K4me2_rep1_chr*.bed Alignments K562 H3K4me2 1 data/Broad_Raw_K562_H3K4me2_rep2_chr*.bed Alignments K562 H3K4me2 2 data/Broad_Raw_K562_H3K4me1_rep1_chr*.bed Alignments K562 H3K4me1 1 data/Broad_Raw_K562_H3K4me1_rep2_chr*.bed Alignments K562 H3K4me1 2 data/Broad_Raw_K562_H3K9ac_rep1_chr*.bed Alignments K562 H3K9ac 1 data/Broad_Raw_K562_H3K9ac_rep2_chr*.bed Alignments K562 H3K9ac 2 data/Broad_Raw_K562_H3K27ac_rep1_chr*.bed Alignments K562 H3K27ac 1 data/Broad_Raw_K562_H3K27ac_rep2_chr*.bed Alignments K562 H3K27ac 2 data/Broad_Raw_K562_H3K27me3_rep1_chr*.bed Alignments K562 H3K27me3 1 data/Broad_Raw_K562_H3K27me3_rep2_chr*.bed Alignments K562 H3K27me3 2 data/Broad_Raw_K562_H3K36me3_rep1_chr*.bed Alignments K562 H3K36me3 1 data/Broad_Raw_K562_H3K36me3_rep2_chr*.bed Alignments K562 H3K36me3 2 data/Broad_Raw_K562_H3K9me1_rep1_chr*.bed Alignments K562 H3K9me1 1 data/Broad_Raw_K562_H3K9me1_rep2_chr*.bed Alignments K562 H3K9me1 2 data/Broad_Raw_K562_H4K20me1_rep1_chr*.bed Alignments K562 H4K20me1 1 data/Broad_Raw_K562_H4K20me1_rep2_chr*.bed Alignments K562 H4K20me1 2 data/Broad_Raw_K562_CTCF_rep1_chr*.bed Alignments K562 CTCF 1 data/Broad_Raw_K562_CTCF_rep2_chr*.bed Alignments K562 CTCF 2 data/Broad_Raw_K562_Pol2_rep1_chr*.bed Alignments K562 Pol2(b) 1 data/Broad_Raw_K562_Pol2_rep2_chr*.bed Alignments K562 Pol2(b) 2 data/Broad_Raw_K562_WCE_rep1_chr*.bed Alignments K562 Control 1 data/Broad_Raw_K562_WCE_rep2_chr*.bed Alignments K562 Control 2 mkdir data cp ../66/data/Broad_Raw_K562_H3K4me3_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K4me3_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K4me2_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K4me2_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K4me1_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K4me1_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K9ac_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K9ac_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K27ac_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K27ac_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K27me3_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K27me3_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K36me3_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K36me3_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K9me1_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H3K9me1_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H4K20me1_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_H4K20me1_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_CTCF_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_CTCF_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_Pol2_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_Pol2_rep2_chr*.bed data/ cp ../66/data/Broad_Raw_K562_WCE_rep1_chr*.bed data/ cp ../66/data/Broad_Raw_K562_WCE_rep2_chr*.bed data/ head -1 ../66/BroadChipSeq.DDF > BroadChipSeq.DDF grep Alignment ../66/BroadChipSeq.DDF >> BroadChipSeq.DDF cp ../66/BroadChipSeq.DAF > BroadChipSeq.DAF edit /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/108 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/108 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/108 > upload_error 2>&1 & Peaks in downloads dir ==================== | 66 | Broad ChIPSeq K562 112008 | displayed | cd 66 data/Broad_K562_CTCF_chr*.pk Peaks K562 CTCF 080608 data/Broad_K562_H3K27ac_chr*.pk Peaks K562 H3K27ac 080608 data/Broad_K562_H3K27me3_chr*.pk Peaks K562 H3K27me3 080608 data/Broad_K562_H3K36me3_chr*.pk Peaks K562 H3K36me3 080608 data/Broad_K562_H3K4me1_chr*.pk Peaks K562 H3K4me1 080608 data/Broad_K562_H3K4me2_chr*.pk Peaks K562 H3K4me2 080608 data/Broad_K562_H3K4me3_chr*.pk Peaks K562 H3K4me3 080608 data/Broad_K562_H3K9ac_chr*.pk Peaks K562 H3K9ac 080608 data/Broad_K562_H3K9me1_chr*.pk Peaks K562 H3K9me1 080608 data/Broad_K562_H4K20me1_chr*.pk Peaks K562 H4K20me1 080608 data/Broad_K562_Pol2_chr*.pk Peaks K562 Pol2(b) 080608 rm tmp.pk touch tmp.pk for F in data/Broad_K562_Pol2_chr*.pk do ll $F cat $F >> tmp.pk done ll tmp.pk /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562Ctcf.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k27ac.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k27me3.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k36me3.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k4me1.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k4me2.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k4me3.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k9ac.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k9me1.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H4k20me1.broadPeak.gz & /bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562Pol2b.broadPeak.gz & Broad Again 2009-01-05 ====================== | wgEncodeBroadChipSeqPeaksK562Ctcf | | wgEncodeBroadChipSeqPeaksK562H3k27ac | | wgEncodeBroadChipSeqPeaksK562H3k27me3 | | wgEncodeBroadChipSeqPeaksK562H3k36me3 | | wgEncodeBroadChipSeqPeaksK562H3k4me1 | | wgEncodeBroadChipSeqPeaksK562H3k4me2 | | wgEncodeBroadChipSeqPeaksK562H3k4me3 | | wgEncodeBroadChipSeqPeaksK562H3k9ac | | wgEncodeBroadChipSeqPeaksK562H3k9me1 | | wgEncodeBroadChipSeqPeaksK562H4k20me1 | | wgEncodeBroadChipSeqPeaksK562Pol2b | | wgEncodeBroadChipSeqRawSignalRep1K562Control | | wgEncodeBroadChipSeqRawSignalRep1K562Ctcf | | wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac | | wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3 | | wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac | | wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1 | | wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1 | | wgEncodeBroadChipSeqRawSignalRep1K562Pol2b | | wgEncodeBroadChipSeqRawSignalRep2K562Control | | wgEncodeBroadChipSeqRawSignalRep2K562Ctcf | | wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac | | wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3 | | wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac | | wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1 | | wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1 | | wgEncodeBroadChipSeqRawSignalRep2K562Pol2b | | wgEncodeBroadChipSeqSignalK562Ctcf | | wgEncodeBroadChipSeqSignalK562H3k27ac | | wgEncodeBroadChipSeqSignalK562H3k27me3 | | wgEncodeBroadChipSeqSignalK562H3k36me3 | | wgEncodeBroadChipSeqSignalK562H3k4me1 | | wgEncodeBroadChipSeqSignalK562H3k4me2 | | wgEncodeBroadChipSeqSignalK562H3k4me3 | | wgEncodeBroadChipSeqSignalK562H3k9ac | | wgEncodeBroadChipSeqSignalK562H3k9me1 | | wgEncodeBroadChipSeqSignalK562H4k20me1 | | wgEncodeBroadChipSeqSignalK562Pol2b | #rename table wgEncodeBroadChipSeqRawSignalRep1K562Control to sav_wgEncodeBroadChipSeqRawSignalRep1K562Control ; #rename table wgEncodeBroadChipSeqRawSignalRep2K562Control to sav_wgEncodeBroadChipSeqRawSignalRep2K562Control ; rename table wgEncodeBroadChipSeqPeaksK562Ctcf to sav_wgEncodeBroadChipSeqPeaksK562Ctcf; rename table wgEncodeBroadChipSeqPeaksK562H3k27ac to sav_wgEncodeBroadChipSeqPeaksK562H3k27ac ; rename table wgEncodeBroadChipSeqPeaksK562H3k27me3 to sav_wgEncodeBroadChipSeqPeaksK562H3k27me3 ; rename table wgEncodeBroadChipSeqPeaksK562H3k36me3 to sav_wgEncodeBroadChipSeqPeaksK562H3k36me3 ; rename table wgEncodeBroadChipSeqPeaksK562H3k4me1 to sav_wgEncodeBroadChipSeqPeaksK562H3k4me1 ; rename table wgEncodeBroadChipSeqPeaksK562H3k4me2 to sav_wgEncodeBroadChipSeqPeaksK562H3k4me2 ; rename table wgEncodeBroadChipSeqPeaksK562H3k4me3 to sav_wgEncodeBroadChipSeqPeaksK562H3k4me3 ; rename table wgEncodeBroadChipSeqPeaksK562H3k9ac to sav_wgEncodeBroadChipSeqPeaksK562H3k9ac ; rename table wgEncodeBroadChipSeqPeaksK562H3k9me1 to sav_wgEncodeBroadChipSeqPeaksK562H3k9me1 ; rename table wgEncodeBroadChipSeqPeaksK562H4k20me1 to sav_wgEncodeBroadChipSeqPeaksK562H4k20me1 ; rename table wgEncodeBroadChipSeqPeaksK562Pol2b to sav_wgEncodeBroadChipSeqPeaksK562Pol2b ; rename table wgEncodeBroadChipSeqRawSignalRep1K562Ctcf to sav_wgEncodeBroadChipSeqRawSignalRep1K562Ctcf ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1 ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2 ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3 ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1 ; rename table wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1; rename table wgEncodeBroadChipSeqRawSignalRep1K562Pol2b to sav_wgEncodeBroadChipSeqRawSignalRep1K562Pol2b ; rename table wgEncodeBroadChipSeqRawSignalRep2K562Ctcf to sav_wgEncodeBroadChipSeqRawSignalRep2K562Ctcf ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1 ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2 ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3 ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1 ; rename table wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1; rename table wgEncodeBroadChipSeqRawSignalRep2K562Pol2b to sav_wgEncodeBroadChipSeqRawSignalRep2K562Pol2b ; rename table wgEncodeBroadChipSeqSignalK562Ctcf to sav_wgEncodeBroadChipSeqSignalK562Ctcf ; rename table wgEncodeBroadChipSeqSignalK562H3k27ac to sav_wgEncodeBroadChipSeqSignalK562H3k27ac ; rename table wgEncodeBroadChipSeqSignalK562H3k27me3 to sav_wgEncodeBroadChipSeqSignalK562H3k27me3 ; rename table wgEncodeBroadChipSeqSignalK562H3k36me3 to sav_wgEncodeBroadChipSeqSignalK562H3k36me3 ; rename table wgEncodeBroadChipSeqSignalK562H3k4me1 to sav_wgEncodeBroadChipSeqSignalK562H3k4me1 ; rename table wgEncodeBroadChipSeqSignalK562H3k4me2 to sav_wgEncodeBroadChipSeqSignalK562H3k4me2 ; rename table wgEncodeBroadChipSeqSignalK562H3k4me3 to sav_wgEncodeBroadChipSeqSignalK562H3k4me3 ; rename table wgEncodeBroadChipSeqSignalK562H3k9ac to sav_wgEncodeBroadChipSeqSignalK562H3k9ac ; rename table wgEncodeBroadChipSeqSignalK562H3k9me1 to sav_wgEncodeBroadChipSeqSignalK562H3k9me1 ; rename table wgEncodeBroadChipSeqSignalK562H4k20me1 to sav_wgEncodeBroadChipSeqSignalK562H4k20me1 ; rename table wgEncodeBroadChipSeqSignalK562Pol2b to sav_wgEncodeBroadChipSeqSignalK562Pol2b ; /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/149 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/149 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/149 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/150 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/151 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/152 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/153 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/154 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/155 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/156 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/157 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/158 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/159 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/160 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/161 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/150 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/150 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/151 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/151 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/152 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/152 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/153 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/153 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/154 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/154 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/155 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/155 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/156 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/156 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/157 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/157 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/158 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/158 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/159 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/159 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/160 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/160 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/161 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/161 > upload_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/173 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/174 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/175 > validate_error 2>&1 tar -cpzf redoHuvecControl.tgz BroadChipSeqControl.DAF BroadChipSeqControl.DDF mv redoHuvecControl.tgz ../../ftp/prod/tarjei/ tar -cpzf redoNHekH3K4me3.tgz BroadChipSeq.DDF mv redoNHekH3K4me3.tgz ../../ftp/prod/tarjei/ tar -cpzf redoNHekH3K4me2.tgz BroadChipSeq.DDF mv redoNHekH3K4me2.tgz ../../ftp/prod/tarjei/ /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/185 > validate_error 2>&1 tar -cpzf redoKeratinocyteControl.tgz BroadChipSeqControl.DAF BroadChipSeqControl.DDF mv redoKeratinocyteControl.tgz ../../ftp/prod/tarjei/ Last in trachkDb.ra: 160, 181 Broad first release to RR 4/6/2009 ================================== /cluster/data/encode/pipeline/bin/encodeStatus.pl 140 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 141 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 142 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 143 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 144 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 145 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 146 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 147 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 148 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 149 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 150 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 151 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 152 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 153 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 154 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 155 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 156 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 157 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 158 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 159 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 160 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 161 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 162 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 163 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 164 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 165 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 166 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 167 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 168 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 169 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 170 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 171 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 172 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 173 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 174 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 175 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 176 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 177 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 178 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 179 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 180 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 181 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 182 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 183 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 184 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 185 released Investigation of bedItemOverlapCount bug 2009-05-01 ==================================================== /cluster/bin/x86_64/bedExtendRanges hg18 300 data/Broad_Raw_GM12878_H3K4me1_rep1_chr22.bed data/Broad_Raw_GM12878_H3K4me1_rep1_chrX.bed | sort -S 5G -T /data/tmp -k1,1 -k2,2n > manualSort.bed bedItemOverlapCount -verbose=2 hg18 manualSort.bed > manualRawSignal1.bed ~/bin/x86_64/bedItemOverlapCount -verbose=2 hg18 manualSort.bed > manualRawSignal1.bed /cluster/bin/x86_64/bedExtendRanges hg18 300 data/Broad_Raw_GM12878_H3K4me1_rep1_chr22.bed data/Broad_Raw_GM12878_H3K4me1_rep1_chrX.bed | sort -S 5G -T /data/tmp -k1,1 -k2,2n - | grep -v -E "^track" | bedItemOverlapCount -verbose=2 hg18 stdin > manualRawSignal1.bed Regenerate Raw Signals because of bug in bedOverlap 2009-05-11 ============================================================== # Can't rename sig because wigs are attached to files. The regeneration will merely add some data to the end of chrX. # Could fly without a net and regen to the same name or could regen to Rel2, even though there is no real difference. # Regen to Rel to requires release alpha/beta but so be it. List of table: subId=140 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me3 fragLength=300 subId=140 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3 fragLength=300 subId=141 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me2 fragLength=300 subId=141 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2 fragLength=300 subId=142 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me1 fragLength=300 subId=142 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1 fragLength=300 subId=143 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k36me3 fragLength=300 subId=143 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3 fragLength=300 subId=144 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27me3 fragLength=300 subId=144 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3 fragLength=300 subId=145 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27ac fragLength=300 subId=145 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac fragLength=300 subId=146 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k9ac fragLength=300 subId=146 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac fragLength=300 subId=147 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1 fragLength=300 subId=147 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1 fragLength=300 subId=148 wgEncodeBroadChipSeqAlignmentsRep1Gm12878Ctcf fragLength=300 subId=148 wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf fragLength=300 subId=149 wgEncodeBroadChipSeqAlignmentsRep1Gm12878Control fragLength=300 subId=149 wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control fragLength=300 subId=150 wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me3 fragLength=300 subId=150 wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me3 fragLength=300 subId=151 wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me2 fragLength=300 subId=151 wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me2 fragLength=300 subId=152 wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me1 fragLength=300 subId=152 wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me1 fragLength=300 subId=153 wgEncodeBroadChipSeqAlignmentsRep1K562H3k27me3 fragLength=300 subId=153 wgEncodeBroadChipSeqAlignmentsRep2K562H3k27me3 fragLength=300 subId=154 wgEncodeBroadChipSeqAlignmentsRep1K562H3k36me3 fragLength=300 subId=154 wgEncodeBroadChipSeqAlignmentsRep2K562H3k36me3 fragLength=300 subId=155 wgEncodeBroadChipSeqAlignmentsRep1K562H3k9ac fragLength=300 subId=155 wgEncodeBroadChipSeqAlignmentsRep2K562H3k9ac fragLength=300 subId=156 wgEncodeBroadChipSeqAlignmentsRep1K562H3k27ac fragLength=300 subId=156 wgEncodeBroadChipSeqAlignmentsRep2K562H3k27ac fragLength=300 subId=157 wgEncodeBroadChipSeqAlignmentsRep1K562Ctcf fragLength=300 subId=157 wgEncodeBroadChipSeqAlignmentsRep2K562Ctcf fragLength=300 subId=158 wgEncodeBroadChipSeqAlignmentsRep1K562H3k9me1 fragLength=300 subId=158 wgEncodeBroadChipSeqAlignmentsRep2K562H3k9me1 fragLength=300 subId=159 wgEncodeBroadChipSeqAlignmentsRep1K562H4k20me1 fragLength=300 subId=159 wgEncodeBroadChipSeqAlignmentsRep2K562H4k20me1 fragLength=300 subId=160 wgEncodeBroadChipSeqAlignmentsRep1K562Pol2b fragLength=300 subId=160 wgEncodeBroadChipSeqAlignmentsRep2K562Pol2b fragLength=300 subId=161 wgEncodeBroadChipSeqAlignmentsRep1K562Control fragLength=300 subId=161 wgEncodeBroadChipSeqAlignmentsRep2K562Control fragLength=300 subId=162 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me3 fragLength=300 subId=162 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3 fragLength=300 subId=163 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me2 fragLength=300 subId=163 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2 fragLength=300 subId=164 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me1 fragLength=300 subId=164 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1 fragLength=300 subId=165 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27me3 fragLength=300 subId=165 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3 fragLength=300 subId=166 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k36me3 fragLength=300 subId=166 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3 fragLength=300 subId=167 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9ac fragLength=300 subId=167 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9ac fragLength=300 subId=168 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27ac fragLength=300 subId=168 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27ac fragLength=300 subId=169 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9me1 fragLength=300 subId=169 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1 fragLength=300 subId=170 wgEncodeBroadChipSeqAlignmentsRep1HuvecH4k20me1 fragLength=300 subId=170 wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1 fragLength=300 subId=171 wgEncodeBroadChipSeqAlignmentsRep1HuvecCtcf fragLength=300 subId=171 wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcf fragLength=300 subId=172 wgEncodeBroadChipSeqAlignmentsRep1HuvecPol2b fragLength=300 subId=172 wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2b fragLength=300 subId=173 wgEncodeBroadChipSeqAlignmentsRep1HuvecControl fragLength=300 subId=173 wgEncodeBroadChipSeqAlignmentsRep2HuvecControl fragLength=300 subId=174 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me3 fragLength=300 subId=174 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me3 fragLength=300 subId=175 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me2 fragLength=300 subId=175 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me2 fragLength=300 subId=176 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me1 fragLength=300 subId=176 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me1 fragLength=300 subId=177 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27me3 fragLength=300 subId=177 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27me3 fragLength=300 subId=178 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k36me3 fragLength=300 subId=178 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k36me3 fragLength=300 subId=179 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9ac fragLength=300 subId=179 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9ac fragLength=300 subId=180 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27ac fragLength=300 subId=180 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27ac fragLength=300 subId=181 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9me1 fragLength=300 subId=181 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9me1 fragLength=300 subId=182 wgEncodeBroadChipSeqAlignmentsRep1NhekH4k20me1 fragLength=300 subId=182 wgEncodeBroadChipSeqAlignmentsRep2NhekH4k20me1 fragLength=300 subId=183 wgEncodeBroadChipSeqAlignmentsRep1NhekCtcf fragLength=300 subId=183 wgEncodeBroadChipSeqAlignmentsRep2NhekCtcf fragLength=300 subId=184 wgEncodeBroadChipSeqAlignmentsRep1NhekPol2b fragLength=300 subId=184 wgEncodeBroadChipSeqAlignmentsRep2NhekPol2b fragLength=300 subId=185 wgEncodeBroadChipSeqAlignmentsRep1NhekControl fragLength=300 subId=185 wgEncodeBroadChipSeqAlignmentsRep2NhekControl fragLength=300 List of submission dirs: 140-185 # make rawSigBroad.D*F tar -cpzf rawSigBroad.tgz rawSigBroad.D*F Made new submission dir=332 # Move superceded dir out of the way: cd encpipeline_prod mv 66 superceded/ mv 108 superceded/ validate errors: ERROR: failed validateTagAlign : Error [file=../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr11.bed, line=229165]: end(134452385) > chromSize(chr11=134452384) [chr11 134452333 134452385 TAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 1000 +] Aborting ... found 1 errors in total grep chromSize validate_error | grep -v chr11 | grep -v chr7 | grep -v chr10 | grep -v chr15 | grep -v chr21 | grep -v chr18 | grep -v chrX| wc -l 0 chr7,chr10,chr15,chr10,chr11,chr18,chr21 Sequences length 51, end - start = 52 Bad news Are they all 51/52? awk '{printf "%d\n",$3 - $2;}' ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed | uniq -c | wc -l 1 awk '{printf "%d\n",$3 - $2;}' ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed | head 52 52 head ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed chr1 68004439 68004491 AGACAAGCCCCTTTCAACGTCCCACCCAATTATCGGCTGACAAACTTTCCA 1000 + chr1 216184249 216184301 CTATAATCCCAGCTACTTGGAAGGCTGAGGCAGGAGAATCGCTTGAACCTG 1000 - head ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed | awk '{printf "%s\t%d\t%d\t%s\t%d\t%s\n",$1,$2,$3 - 1,$4,$5,$6;}' chr1 68004439 68004490 AGACAAGCCCCTTTCAACGTCCCACCCAATTATCGGCTGACAAACTTTCCA 1000 + chr1 216184249 216184300 CTATAATCCCAGCTACTTGGAAGGCTGAGGCAGGAGAATCGCTTGAACCTG 1000 - ### So it appears that all Broad tagAlign files have and end position 1 past where it should be !!! # it also appears that this can be remedied here, but not without a lot of processing. # created 332/fixTagAlign.sh script for all of the Broad tagAlign files Generate RawSignal files for download 2009-5-28 =============================================== from pip grep RawSignal 332/out/load.ra | grep auto >> 325/out/mkRawSigsFiles.sh grep RawSignal 332/out/load.ra | grep wgEncode >> 325/out/mkRawSigsFiles.sh ... Edit and then run 332/out/mkRawSigsFiles.sh placing *.wig.gz into downloads/wgEncodeBroadChipSeq/raw cd downloads/wgEncodeBroadChipSeq/raw cp ../preamble.html cp ../fileDb.ra edit preamble.html to note the subdirectory only contains Raw Signals encodeDownloadsPage.pl index.html mkdir old mv *.tagAlign.gz old mv ../wgEncodeBoradChipSeqRel2/*.tagAlign.gz . grep metatdata /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.ra | grep tagAlign > /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.tagAgling.ra # edit /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.tagAgling.ra grep metatdata /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.tagAgling.ra >> fileDb.ra encodeDownloadsPage.pl index.html /cluster/data/encode/pipeline/bin/encodeStatus.pl 332 displayed Tarjei sends alignability track as tar.gz 2009-06-02 ==================================================== # in /cse/staff/tdreszer/docs/ENCODE/broad/mapability tar -xzf Broad_Alignable.tar.gz cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/107/DukeExtraTracks.DAF broadAlignability.DAF cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/107/DukeExtraTracks.DDF broadAlignability.DDF # edit DDF and DAF tar -cpzf broadAlignability.tgz broadAlignability.DAF broadAlignability.DDF Broad_Alignable_chr*.wig # log into submission page as tarjei and submit this rename table wgEncodeBroadMapabilityAlignability36bpReferencegenome to wgEncodeBroadMapabilityAlign36mer; update wgEncodeBroadMapabilityAlign36mer set file = "/gbdb/hg18/wib/wgEncodeBroadMapabilityAlign36mer.wib"; cd 344 mv wgEncodeBroadMapabilityAlignability36bpReferencegenome.wib wgEncodeBroadMapabilityAlign36mer.wib rm /gbdb/hg18/wib/wgEncodeBroadMapabilityAlignability36bpReferencegenome.wib cd /gbdb/hg18/wib ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/344/wgEncodeBroadMapabilityAlign36mer.wib wgEncodeBroadMapabilityAlign36mer.wib # in downloads dir: wgEncodeMapability mv ../wgEncodeBroadMapability/wgEncodeBroadMapabilityAlignability36bpReferencegenome.wib wgEncodeBroadMapabilityAlign36mer.wib # edit trackDb.wgEncode.ra make alpha DBS=hg18 encodeDownloadsPage.pl index.html /cluster/data/encode/pipeline/bin/encodeStatus.pl 344 displayed # quicky for broad validateFiles -type=tagAlign -genome=/cluster/data/hg18/hg18.2bit -mismatches=3 -nMatch -matchFirst=25 -mmCheckOneInN=100 wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocytePol2b.tagAlign.gz Works! head -2 Broad_Raw_HMEC_CTCF_rep1_chr1.bed chr1 13 48 TAACCCTAACCCTAACCCTAACCCTAACCCTAACNC 1000 + chr1 62 97 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCT 1000 - head -2 Broad_Raw_HMEC_CTCF_rep1_chr1.bed | awk '{printf "%s\t%d\t%d\t%s\t%d\t%s\n",$1,$2 - 1,$3,$4,$5,$6;}' chr1 12 48 TAACCCTAACCCTAACCCTAACCCTAACCCTAACNC 1000 + chr1 61 97 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCT 1000 - /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x ../551 head -2 Broad_Raw_HMEC_CTCF_rep1_chr1new2.bed | awk '{printf "%s\t%d\t%d\t%s\t%d\t+\n",$1,$2,$3,$4,$5;}' 2009-09-27 Noam Shoresh is loading up for Sept freeze ===================================================== # First submissions failed on tagAligns 1) Half open error 2) Negative strand was double reversed: ERROR: failed validateTagAlign : Error [file=data/Broad_Raw_HMEC_CTCF_rep1_chr1new.bed, line=200]: too many mismatches (found 22 /36, maximum is 3) (chr1 15955 15991 -) seq=[CTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTT] gen=[aaggaggaactcactgaaaagtgctggcctgaggag] These are all negative strand problems. The tagAlign should have the actual sequence that the sequencer came up with. The same one as found in the fastq (unaligned). But it looks like you reversed the sequence in both senses of the word. That is the sequence char1 15955 15991 CTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTT - should have been char1 15955 15991 AAGGAGGAACTCACTGAAAAGTGCTGGCCTGAGGAG - Noam fixed these and is resubmitting. His first one after this loads fine. Broad also has the outstanding sparse signal error: From the looks of the data, every *.wig file has a first line something like: fixedStep chrom=chr3 start=1 step=25 But should have a first line something like: fixedStep chrom=chr3 start=1 step=25 span=25 This means the first value will be set for positions 1-25 and the second will be set for 26-50. What Broad is currently submitting will set a value at 1 then 26,.... It will leave positions 2-25 valueless! This is not a problem and the Broad signal graphs are still interpretable. But I believe Broad's intention is to show continuous signal across the whole chromosome, but what they are showing is a discrete signal of 1 base in length at 25 base intervals. Response from Noam 9-28-2009: I forgot about the wig files... But it is, in fact, with gaps, that we usually look at these data, so this is intentional. In a way it might make a bit more sense to change it... but for consistency's sake, and to save me some hassle right now, let's keep it as is. -tim: Agreed. 2009-10-02 Melissa got the tracks loaded int trackDb ==================================================== select id,name,status from projects where status = "loaded" and name like "Broad%"; | 554 | BroadChipSeq_HMEC_CTCF_092709 | loaded | | 558 | BroadChipSeq_HMEC_WCE_092809 | loaded | | 559 | BroadChipSeq_HepG2_WCE_092809.tgz | loaded | | 561 | BroadChipSeq_HepG2_H3K9ac_092809 | loaded | | 562 | BroadChipSeq_HMEC_H3K27me3_092809 | loaded | | 563 | BroadChipSeq_HepG2_CTCF_092809 | loaded | | 564 | BroadChipSeq_H1_H3K27me3_092809 | loaded | | 565 | BroadChipSeq_HMEC_H3K4me3_092809 | loaded | | 566 | BroadChipSeq_H1_H3K4me3_092809 | loaded | | 567 | BroadChipSeq_HepG2_H3K36me3_092809 | loaded | | 568 | BroadChipSeq_HMEC_H3K36me3_092809 | loaded | | 569 | BroadChipSeq_HMEC_H3K9ac_092809 | loaded | | 570 | BroadChipSeq_HMEC_H3K27ac_092809 | loaded | | 571 | BroadChipSeq_H1_H3K4me1_092809 | loaded | | 572 | BroadChipSeq_HepG2_H3K4me2_092809 | loaded | | 573 | BroadChipSeq_HMEC_H3K4me2_092809 | loaded | | 574 | BroadChipSeq_HMEC_H3K4me1_092809 | loaded | | 575 | BroadChipSeq_NHLF_H3K9ac_092809 | loaded | | 576 | BroadChipSeq_HepG2_H3K27ac_092809 | loaded | | 577 | BroadChipSeq_NHLF_H3K4me1_092809 | loaded | | 578 | BroadChipSeq_NHLF_H3K4me3_092809 | loaded | | 579 | BroadChipSeq_NHLF_H4K20me1_092809 | loaded | | 580 | BroadChipSeq_HMEC_H4K20me1_092809 | loaded | | 581 | BroadChipSeq_HepG2_H3K4me3_092809 | loaded | | 582 | BroadChipSeq_NHLF_H3K27ac_092809 | loaded | | 583 | BroadChipSeq_NHLF_H3K36me3_092809 | loaded | | 584 | BroadChipSeq_NHLF_H3K4me2_092809 | loaded | | 585 | BroadChipSeq_H1_CTCF_092809 | loaded | | 586 | BroadChipSeq_HepG2_H4K20me1_092809 | loaded | | 616 | BroadChipSeq_H1_WCE_092809 | loaded | | 617 | BroadChipSeq_NHLF_WCE_092809 | loaded | | 618 | BroadChipSeq_NHLF_H3K27me3_092809 | loaded | | 619 | BroadChipSeq_H1_H4K20me1_092809 | loaded | /cluster/data/encode/pipeline/bin/encodeStatus.pl 554 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 558 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 559 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 561 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 562 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 563 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 564 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 565 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 566 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 567 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 568 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 569 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 570 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 571 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 572 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 573 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 574 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 575 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 576 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 577 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 578 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 579 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 580 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 581 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 582 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 583 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 584 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 585 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 586 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 616 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 617 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 618 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 619 displayed 2009-10-07 Noam realized the peaks were wrong ============================================= Had him submit them all to 1 new dir. Expected and got validation failed because old tables were in the way validated the new data only touches unreleased data modified daf with "allowReloads" revalidated... loaded fine /cluster/data/encode/pipeline/bin/encodeStatus.pl 668 displayed remodified daf to remove "allowReloads" to avoid future accidents 2009-10-09 Aproval ================== /cluster/data/encode/pipeline/bin/encodeStatus.pl 558 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 332 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 559 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 554 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 561 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 562 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 563 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 564 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 565 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 566 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 567 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 568 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 569 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 571 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 570 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 572 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 573 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 574 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 575 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 576 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 577 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 578 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 579 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 580 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 581 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 582 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 583 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 584 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 585 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 586 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 616 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 617 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 618 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 619 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 668 approved 2009-10-14 Make release1 downloads dir to prepare for release2 ============================================================== cd {downloadsDir}/wgEncodeBroadChIPseq/ mkdir release1 cp preamble.html release1/ cp fileDb.ra release1/ # In RR browser, go to downloads page and save source into release1/ as index.html # Use that list as complete set of *.gz files that should be in release1 # Attempt to link them from downloads dir. If this fails, then mv from old: mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878Control.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878Ctcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecControl.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecCtcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecPol2b.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562Control.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562Ctcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k9me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562Pol2b.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekControl.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekCtcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekPol2b.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecControl.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2b.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562Control.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562Ctcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k9me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562Pol2b.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekControl.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekCtcf.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k36me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me2.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me3.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9ac.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH4k20me1.tagAlign.gz . mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekPol2b.tagAlign.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878Ctcf.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k27ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k27me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k36me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k4me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k4me2.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k4me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H3k9ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksGm12878H4k20me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecCtcf.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k27ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k27me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k36me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k4me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k4me2.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k4me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k9ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH3k9me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecH4k20me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksHuvecPol2b.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562Ctcf.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k27ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k27me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k36me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k4me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k4me2.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k4me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k9ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H3k9me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562H4k20me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksK562Pol2b.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekCtcf.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k27ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k27me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k36me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k4me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k4me2.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k4me3.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k9ac.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH3k9me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekH4k20me1.broadPeak.gz . ln ../wgEncodeBroadChipSeqPeaksNhekPol2b.broadPeak.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878Control.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878Ctcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecControl.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecCtcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k9me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1HuvecPol2b.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562Control.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562Ctcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k9me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562H4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1K562Pol2b.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekControl.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekCtcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k9me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekH4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep1NhekPol2b.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878Control.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878Ctcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecControl.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecCtcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k9me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2HuvecPol2b.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562Control.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562Ctcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k9me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562H4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2K562Pol2b.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekControl.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekCtcf.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k27ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k27me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k36me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k4me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k4me2.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k4me3.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k9ac.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k9me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekH4k20me1.fastq.gz . ln ../wgEncodeBroadChipSeqRawDataRep2NhekPol2b.fastq.gz . ln ../wgEncodeBroadChipSeqSignalGm12878Control.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878Ctcf.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k27ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k27me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k36me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k4me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k4me2.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k4me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H3k9ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalGm12878H4k20me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecControl.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecCtcf.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k27ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k27me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k36me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k4me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k4me2.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k4me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k9ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH3k9me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecH4k20me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalHuvecPol2b.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562Control.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562Ctcf.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k27ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k27me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k36me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k4me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k4me2.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k9ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562H4k20me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalK562Pol2b.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekControl.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekCtcf.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k27ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k27me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k36me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k4me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k4me2.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k4me3.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k9ac.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH3k9me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekH4k20me1.wig.gz . ln ../wgEncodeBroadChipSeqSignalNhekPol2b.wig.gz . # Notice the only versioned data is the tagAligns. # Replace "Rel2" with "V2" (wished I had done this with Yale) # No tables involved! mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878Control.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878ControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878Ctcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878CtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecControl.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecCtcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecCtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k9me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecH4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecPol2b.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1HuvecPol2bV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562Control.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562ControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562Ctcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562CtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k9me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562H4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562Pol2b.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1K562Pol2bV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteControl.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteCtcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteCtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k9me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocytePol2b.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878Control.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878Ctcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecControl.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecCtcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k9me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecPol2b.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2bV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562Control.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562ControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562Ctcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562CtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k9me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562H4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562Pol2b.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2K562Pol2bV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteControl.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteControlV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteCtcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteCtcfV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k27acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k27me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k36me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k4me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k4me2V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k4me3V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k9acV2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k9me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocytePol2b.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAlign.gz ls *V2.* | wc -l 92 ls *Rel2*.gz | wc -l 0 grep Rel2 fileDb.ra | wc -l 92 grep Rel2 fileDb.ra > tmpRel2.txt grep -v Rel2 fileDb.ra > fileDb.ra.new cp fileDb.ra fileDb.ra.2009-10-14 # edit tmpRel2.txt to replace Rel2 with V2 and add 'submittedDataVersion="V2 - corrected off-by-one error in end position"' cat tmpRel2.txt >> fileDb.ra.new mv fileDb.ra.new fileDb.ra # Add a note to the preamble.html to describe the correction on the older tagAligns, and declare this as a "release 2". encodeDownloadsPage.pl index.html #Filter ranges: select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878Ctcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k27me3; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k36me3; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H4k20me1; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescCtcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH3k27me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH4k20me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2Ctcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k36me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H4k20me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecCtcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k27me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k36me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH4k20me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecCtcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k27me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k36me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k9me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH4k20me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecPol2b ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562Ctcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k27me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k36me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k9me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H4k20me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562Pol2b ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekCtcf ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k27me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k36me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k9me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH4k20me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekPol2b ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k27ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k27me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k36me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k4me1 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k4me2 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k4me3 ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k9ac ; select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH4k20me1 ; # Result score 1000:1000, signalValue 0:45000 (but too variable to be useful) pValue 0:100, qValue -1:-1 2009-11-05 In QA (some time ago actually) ========================================= select id,name,status from projects where status not in ("displayed","released","revoked","superseded","reviewing"); | 81 | /cluster/data/encode/pipeline/bin/encodeStatus.pl 558 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 332 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 559 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 554 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 561 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 562 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 563 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 564 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 565 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 566 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 567 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 568 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 569 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 571 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 570 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 572 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 573 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 574 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 575 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 576 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 577 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 578 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 579 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 580 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 581 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 582 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 583 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 584 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 585 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 586 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 616 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 617 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 618 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 619 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 668 reviewing select id,name,status from projects where status not in ("displayed","released","revoked","superseded","reviewing"); | 46 | 2009-11-30 Missing GM12878 Rep2 tagAligns! ========================================== Downloads dir has only one (V2) subId=332 sub 332 regenerated Raw from already submitted tagAligns, so there should be no V2 sub 332 was the old fashion Rel2 downloadsDir/release1 has all original which should be the ones! ln ln release1/wgEncodeBroadChipSeqAlignmentsRep2Gm12878*.tagAlign.gz . ### NO THIS is not so: zcat wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1V2.tagAlign.gz | wl 13632898 zcat release1/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1.tagAlign.gz | wl 13632898 zcat wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1V2.tagAlign.gz | head chr1 31659966 31660013 GAATGAGATCAGCATAGACAGCACAGAGAGGCAAGAGAGCCTCTCGC 1000 + zcat release1/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1.tagAlign.gz | head chr1 31659966 31660014 GAATGAGATCAGCATAGACAGCACAGAGAGGCAAGAGAGCCTCTCGC 1000 + ### There is an off by one error. Therefore all V2s are valid. I must remove the ones I just linkined in from release1 and then reload the missing ones! ls *Rep2Gm12878*.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac.tagAlign.gz rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz What is missing exactly? wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz cd {pip}/332 edit DAF/DDF tar -cpzf BroadResubmitTagAlignRep2s.tgz rawSigBroad.DAF rawSigBroad.DDF # submitted to 800 ll *Rep2Gm12878*.tagAlign.gz -rw-rw-r-- 1 qateam protein 198204132 Nov 30 15:31 wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz -rw-rw-r-- 1 qateam protein 235330617 Nov 30 15:02 wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz -rw-rw-r-- 1 qateam protein 207339598 Nov 30 15:15 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz -rw-rw-r-- 1 qateam protein 225546215 Nov 30 15:13 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 295145342 Nov 30 15:22 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 290389709 Nov 30 15:34 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 197423654 Nov 30 15:08 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 203798428 Nov 30 15:10 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 219338761 Nov 30 15:37 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz -rw-rw-r-- 1 qateam protein 268390362 Nov 30 15:39 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz ll *Rep2Huvec*.tagAlign.gz -rw-rw-r-- 2 qateam protein 215910513 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecControlV2.tagAlign.gz -rw-rw-r-- 2 qateam protein 255146612 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcfV2.tagAlign.gz -rw-rw-r-- 2 qateam protein 322322114 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27acV2.tagAlign.gz -rw-rw-r-- 1 qateam protein 387746099 Nov 30 15:19 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 377600984 Nov 30 15:29 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 381183723 Nov 30 15:06 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz -rw-rw-r-- 2 qateam protein 313456944 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2V2.tagAlign.gz -rw-rw-r-- 1 qateam protein 363716703 Nov 30 15:25 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz -rw-rw-r-- 2 qateam protein 248141307 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz -rw-rw-r-- 2 qateam protein 281337854 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1V2.tagAlign.gz -rw-rw-r-- 2 qateam protein 298025445 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1V2.tagAlign.gz -rw-rw-r-- 2 qateam protein 356263922 May 15 2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2bV2.tagAlign.gz zcat wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz | head chr1 84721172 84721223 TGGTTGTCAATGGTCTTGGGTACAGGCTTTGGTGGAGCCTAAGTAAAAGAG 1000 - zcat release1/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz | head chr1 84721172 84721224 TGGTTGTCAATGGTCTTGGGTACAGGCTTTGGTGGAGCCTAAGTAAAAGAG 1000 - # Off by one has been corrected! encodeDownloadsPage.pl index.html cp index.html release2/ cd release2/ ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz . # update broadChipSeq.notes.txt in docs # update pushq entry # inform Anshul /cluster/data/encode/pipeline/bin/encodeStatus.pl 800 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 800 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 800 reviewing # give this submission id back to Broad: update projects set user_id = 34 where id = 800; 2009-12-25 Kayla noticed munged names in downloadsDir ===================================================== cd {downloadsDir}/broad wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign. wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign. wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign. wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlig wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAl wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign. wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.g wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.g wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl* ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA* ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlig* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAl* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.* ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign* ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.g* ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign* ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.g* ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign* ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta* ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl* # all full names found (and same sizes as mangled version) found except: ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl* ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA* ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli* ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta* ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl* # remove duplicates rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign. rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign. rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign. rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlig rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAl rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign. rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.g rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.g rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign # rename mangled mv wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAlign.gz mv wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAlign.gz mv wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.tagAlign.gz mv wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAlign.gz # link cd release2/ ln ../wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.tagAlign.gz . ln ../wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAlign.gz . cd .. # edit fileDb.ra replace "cell=Keratinocyte" with "cell=NHEK" encodeDownloadsPage.pl index.html cp index.html release2/ cp fileDb.ra release2/ 2009-12-18 Start of Jan 2010 freeze =================================== select id,name,status from projects where name like "Broad%" and status = "loaded" order by id; +-----+----------------------------+--------+ | id | name | status | +-----+----------------------------+--------+ | 815 | BroadChipSeq_H1_H3K9ac | loaded | | 816 | BroadChipSeq_H1_H3K36me3 | loaded | | 817 | BroadChipSeq_H1_H3K4me2 | loaded | | 818 | BroadChipSeq_NHLF_CTCF | loaded | | 819 | BroadChipSeq_HSMM_H3K36me3 | loaded | | 820 | BroadChipSeq_HSMM_H4K20me1 | loaded | | 821 | BroadChipSeq_HSMM_H3K4me1 | loaded | | 822 | BroadChipSeq_HSMM_H3K27ac | loaded | | 823 | BroadChipSeq_HSMM_H3K27me3 | loaded | | 824 | BroadChipSeq_HSMM_H3K9ac | loaded | | 825 | BroadChipSeq_HSMM_H3K4me2 | loaded | | 826 | BroadChipSeq_HSMM_CTCF | loaded | | 827 | BroadChipSeq_HSMM_WCE | loaded | | 828 | BroadChipSeq_HSMM_H3K4me3 | loaded | +-----+----------------------------+--------+ 14 rows in set (0.00 sec) # added to trackDb.wgEncode.ra, made alpha cd {downloadsDir} cp fileDb.ra fileDb.ra.2009-12-18 rm tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/815/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/816/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/817/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/818/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/819/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/820/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/821/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/822/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/823/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/824/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/825/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/826/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/827/out/fileDb.ra | grep parentTable >> tmp.txt grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/828/out/fileDb.ra | grep parentTable >> tmp.txt # e tmp.txt cat tmp.txt >> fileDb.ra # Eliminated 28 duplicate fileNames in fileDb.ra encodeDownloadsPage.pl index.html /cluster/data/encode/pipeline/bin/encodeStatus.pl 815 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 816 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 817 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 818 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 819 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 820 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 821 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 822 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 823 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 824 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 825 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 826 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 827 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 828 displayed # missing tables on RR HMEC H3K4me3 Signal wgEncodeBroadChipSeqSignalHmecH3k4me3 HMEC H3K9ac Signal wgEncodeBroadChipSeqSignalHmecH3k9ac HMEC H4K20me1 Signal wgEncodeBroadChipSeqSignalHmecH4k20me1 NHLF H3K27ac Signal wgEncodeBroadChipSeqSignalNhlfH3k4me1 NHLF H3K27me3 Signal wgEncodeBroadChipSeqSignalNhlfH3k4me2 NHLF H3K36me3 Signal wgEncodeBroadChipSeqSignalNhlfH3k4me3 NHLF H3K4me1 Signal wgEncodeBroadChipSeqSignalNhlfH3k9ac NHLF H3K4me2 Signal wgEncodeBroadChipSeqSignalNhlfH3k27ac NHLF H3K4me3 Signal wgEncodeBroadChipSeqSignalNhlfH3k27me3 NHLF H3K9ac Signal wgEncodeBroadChipSeqSignalNhlfH3k36me3 NHLF H4K20me1 Signal wgEncodeBroadChipSeqSignalNhlfH4k20me1 NHLF Input Control Signal wgEncodeBroadChipSeqSignalNhlfControl /cluster/data/encode/pipeline/bin/encodeStatus.pl 332 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 344 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 554 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 558 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 559 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 561 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 562 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 563 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 564 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 565 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 566 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 567 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 568 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 569 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 570 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 571 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 572 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 573 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 574 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 575 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 576 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 577 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 578 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 579 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 580 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 581 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 582 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 583 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 584 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 585 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 586 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 616 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 617 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 618 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 619 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 668 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 800 released 2010-01-06 Redo the H1s by request from Noam ============================================ # In pipeline website unload 815,816,817 (which were marked as displayed) Noam resubmitted. validation failed because of trackDb entries # DANGEROUS: in hgsql hg18 select count(*) from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k36me3'; 2 delete from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k36me3'; select count(*) from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k4me2'; 2 delete from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k4me2'; select count(*) from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k9ac'; 2 delete from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k9ac'; # restart in pipeline: successful this time. make alpha DBS=hg18 /cluster/data/encode/pipeline/bin/encodeStatus.pl 815 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 816 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 817 displayed ## At the freeze: select id,name,status,user_id,created_at from projects where status = "displayed" and name like "Broad%" and created_at > date('2009-11-01') order by name; +-----+----------------------------+-----------+---------+---------------------+ | id | name | status | user_id | created_at | +-----+----------------------------+-----------+---------+---------------------+ | 816 | BroadChipSeq_H1_H3K36me3 | displayed | 34 | 2009-12-16 08:20:35 | | 817 | BroadChipSeq_H1_H3K4me2 | displayed | 34 | 2009-12-16 08:37:58 | | 815 | BroadChipSeq_H1_H3K9ac | displayed | 34 | 2009-12-16 06:28:45 | | 826 | BroadChipSeq_HSMM_CTCF | displayed | 34 | 2009-12-16 08:44:21 | | 822 | BroadChipSeq_HSMM_H3K27ac | displayed | 34 | 2009-12-16 08:41:44 | | 823 | BroadChipSeq_HSMM_H3K27me3 | displayed | 34 | 2009-12-16 08:42:36 | | 819 | BroadChipSeq_HSMM_H3K36me3 | displayed | 34 | 2009-12-16 08:39:18 | | 821 | BroadChipSeq_HSMM_H3K4me1 | displayed | 34 | 2009-12-16 08:40:59 | | 825 | BroadChipSeq_HSMM_H3K4me2 | displayed | 34 | 2009-12-16 08:43:37 | | 828 | BroadChipSeq_HSMM_H3K4me3 | displayed | 34 | 2009-12-16 08:45:20 | | 824 | BroadChipSeq_HSMM_H3K9ac | displayed | 34 | 2009-12-16 08:43:09 | | 820 | BroadChipSeq_HSMM_H4K20me1 | displayed | 34 | 2009-12-16 08:40:07 | | 827 | BroadChipSeq_HSMM_WCE | displayed | 34 | 2009-12-16 08:44:54 | | 818 | BroadChipSeq_NHLF_CTCF | displayed | 34 | 2009-12-16 08:38:40 | +-----+----------------------------+-----------+---------+---------------------+ 14 rows ### Post call issues? None! /cluster/data/encode/pipeline/bin/encodeStatus.pl 815 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 816 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 817 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 818 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 819 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 820 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 821 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 822 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 823 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 824 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 825 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 826 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 827 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 828 approved 2010-03-01 Prepare for release 3 ================================ cd downloadsDir mkdir release3 # todo: cd release3 ln ../*.gz . cp ../index.html . cp ../protocol.html . cp ../files.txt . cp ../md5sum.txt . cp ../fileDb.ra . ll *.gz > ../tmp3.txt cd ../release2 ll *.gz > ../tmp2.txt cd .. diff -w tmp2.txt tmp3.txt | grep "<" > tmpOld.txt diff -w tmp2.txt tmp3.txt | grep ">" > tmpNew.txt e tmpOld.txt tmpNew.txt # remove the < & > diff -w tmp3.txt tmpNew.txt | grep "<" > tmpSame.txt e tmpOld.txt tmpNew.txt /cluster/data/encode/pipeline/bin/encodeStatus.pl 818 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 817 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 816 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 815 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 819 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 820 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 821 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 822 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 823 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 824 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 825 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 826 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 827 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 828 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 818 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 817 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 816 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 815 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 819 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 820 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 821 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 822 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 823 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 824 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 825 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 826 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 827 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 828 released 2010-04-13 Loadeing metaTbl for hg18 ==================================== cd {tdb} grep metadata trackdDb.wgencode.ra | grep Broad > testing/metaBroad.txt cd testing # edit remove the dups mdbUpdate hg18 metaBroad.txt cd {downloads} mdbUpdate hg18 fileDb.ra Using table named 'hg18.mdb_tdreszer'. The same variable appears twice: submittedDataVersion="V2 - corrected off-by-one error in end position" and submittedDataVersion="V2 - corrected off-by-one error in end position". Ignoring second value. project=wgEncode grant=Bernstein lab=Broad dataType=ChipSeq cell=HUVEC antibody=H3K9ac fragLength=300 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=332 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 dateResubmitted=2009-05-15 composite=wgEncodeBroadChipSeq parentTable=wgEncodeBroadChipSeqRawSignalRep2HuvecH3k9acV2 fileName=wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz The same variable appears twice: dateSubmitted=2009-01-06 and dateSubmitted=2009-01-06. Ignoring second value. project=wgEncode grant=Bernstein lab=Broad dataType=ChipSeq cell=HUVEC antibody=H3K9ac fragLength=300 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=332 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 dateResubmitted=2009-05-15 composite=wgEncodeBroadChipSeq parentTable=wgEncodeBroadChipSeqRawSignalRep2HuvecH3k9acV2 fileName=wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz The same variable appears twice: dateUnrestricted=2009-10-06 and dateUnrestricted=2009-10-06. Ignoring second value. project=wgEncode grant=Bernstein lab=Broad dataType=ChipSeq cell=HUVEC antibody=H3K9ac fragLength=300 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=332 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 dateResubmitted=2009-05-15 composite=wgEncodeBroadChipSeq parentTable=wgEncodeBroadChipSeqRawSignalRep2HuvecH3k9acV2 fileName=wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz Read 526 metadata objects from hg18 Affected 7792 row(s) in hg18.mdb_tdreszer encodeDownloadsPage.pl -mdb=mdb_tdreszer mdb.html . encodeDownloadsPage.pl -noMdb noMdb.html . wl mdb.html noMdb.html 586 mdb.html 586 noMdb.html diff mdb.html noMdb.html # Only difference is error in old metadata cd {tdb}/testing mdbPrint hg18 -vars="lab=Broad" -ra > mdbBroad.ra Using table named 'hg18.mdb_tdreszer'. objects:641 vars:10531 # Expected 549 Difference? Must be versioned tables and files which were in fileDb.ra but are no longer in the downloads dir. # Clean extra entries? # get downloads dir list cd {downloads} ls -1 *.gz | sort > ~/kent/src/hg/makeDb/trackDb/human/hg18/testing/tmp.txt # get metaTbl list cd {tdb}/testing grep metaObject mdbBroad.ra > tmp2.txt # edit tmp.txt tmp2.txt to strip down to obj names diff tmp.txt tmp2.txt > tmp3.txt # edit tmp3.txt to strip down to obj names wl tmp3.txt 92 tmp3.txt #edit tmp3.txt as: metadata wgEncodeBroadChipSeqAlignmentsRep1Gm12878Control delete mdbUpdate hg18 tmp3.txt Affected 3999 row(s) in hg18.metaTbl_tdreszer mdbPrint hg18 -vars="lab=Broad" -ra > mdbBroad.ra Using table named 'hg18.mdb_tdreszer'. objects:549 vars:8967 cd {downloads} encodeDownloadsPage.pl -mdb=mdb_tdreszer mdbNew.html . diff mdb.html mdbNew.html # no difference cd {tdb}/testing mv testing/mdbBroad.ra . mdbUpdate hg18 -table=mdb mdbBroad.ra Read 549 metadata objects from hg18 Affected 6228 row(s) in hg18.mdb cvs ci mdbBroad.ra 2010-04-23 Standardize to setType, inputType ============================================ mdbPrint hg18 -vars="lab=Broad" -countObjs Using table named 'hg18.mdb_tdreszer'. 549 objects mdbUpdate hg18 -vars="lab=Broad antibody=Input" -var=setType -val=input Using table named 'hg18.mdb_tdreszer'. Affected 45 row(s) in hg18.mdb_tdreszer mdbUpdate hg18 -vars="lab=Broad antibody!=Input" -var=setType -val=exp Using table named 'hg18.mdb_tdreszer'. Affected 504 row(s) in hg18.mdb_tdreszer #mdbUpdate hg18 -vars="lab=Broad setType=input" -var=inputType -val=?? -test #mdbUpdate hg18 -vars="lab=Broad setType=exp" -var=setType -val=exp -test select distinct t1.val cell,t2.val antibody from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj like "wgEncodeBroad%" and t1.obj = t2.obj and t1.var = "cell" and t2.var = "antibody" order by t1.val,t2.val; 93 rows in set (0.05 sec) select distinct t1.val cell from mdb_tdreszer t1 where t1.obj like "wgEncodeBroad%" and t1.var = "cell" order by t1.val; +---------+ | cell | +---------+ | GM12878 | | H1-hESC | | HMEC | | HSMM | | HUVEC | | HepG2 | | K562 | | NHEK | | NHLF | +---------+ 9 rows in set (0.03 sec) mdbUpdate hg18 -vars="lab=Broad cell=GM12878" -var=inputType val=GM12878/Input mdbUpdate hg18 -vars="lab=Broad cell=H1-hESC" -var=inputType val=H1-hESC/Input mdbUpdate hg18 -vars="lab=Broad cell=HMEC " -var=inputType val=HMEC/Input mdbUpdate hg18 -vars="lab=Broad cell=HSMM " -var=inputType val=HSMM/Input mdbUpdate hg18 -vars="lab=Broad cell=HUVEC " -var=inputType val=HUVEC/Input mdbUpdate hg18 -vars="lab=Broad cell=HepG2 " -var=inputType val=HepG2/Input mdbUpdate hg18 -vars="lab=Broad cell=K562 " -var=inputType val=K562/Input mdbUpdate hg18 -vars="lab=Broad cell=NHEK " -var=inputType val=NHEK/Input mdbUpdate hg18 -vars="lab=Broad cell=NHLF " -var=inputType val=NHLF/Input Affected 59 row(s) in hg18.mdb_tdreszer Affected 53 row(s) in hg18.mdb_tdreszer Affected 59 row(s) in hg18.mdb_tdreszer Affected 59 row(s) in hg18.mdb_tdreszer Affected 71 row(s) in hg18.mdb_tdreszer Affected 47 row(s) in hg18.mdb_tdreszer Affected 71 row(s) in hg18.mdb_tdreszer Affected 71 row(s) in hg18.mdb_tdreszer Affected 59 row(s) in hg18.mdb_tdreszer Total: 549 mdbPrint hg18 -vars="lab=Broad" > mdbBroad.ra Using table named 'hg18.mdb_tdreszer'. objects:549 vars:10065 mdbUpdate hg18 table=mdb mdbBroad.ra Read 549 metadata objects from hg18 Affected 1098 row(s) in hg18.mdb cvs ci -m "Extended setType and inputType to Broad" mdbBroad.ra cd {downloadsDir} encodeDownloadsPage.pl -mdb=mdb index.html . 2011-01-21 Broad Chromatin Modelling by HMM for hg18 ==================================================== Submitted to 3446 Changed Encode.pm to accept hg18 Changed some DDF and failed on dataType=ChipSeq requiring an antibody. Changed to dataTypeCombined doEncodeValidate worked so sent it through the pipeline. Loaded! # verified tables exist in hg18 and downloadable files are in hg18 Tables are "bed 9" show tables like "wgEncodeBroadHmm%"; +------------------------------------+ | wgEncodeBroadHmmGm12878HMM | | wgEncodeBroadHmmH1hescHMM | | wgEncodeBroadHmmHepg2HMM | | wgEncodeBroadHmmHmecHMM | | wgEncodeBroadHmmHsmmHMM | | wgEncodeBroadHmmHuvecHMM | | wgEncodeBroadHmmK562HMM | | wgEncodeBroadHmmNhekHMM | | wgEncodeBroadHmmNhlfHMM | +------------------------------------+ select min(score),max(score) from wgEncodeBroadHmmH1hescHMM; +------------+------------+ | min(score) | max(score) | +------------+------------+ | 0 | 0 | +------------+------------+ cd {downloadsHg18}/wgEncodeBroadHmm ll wgEncode* -rw-rw-r-- 1 encodeteam protein 5305015 Jan 21 09:39 wgEncodeBroadHmmGm12878HMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5717187 Jan 21 09:39 wgEncodeBroadHmmH1hescHMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5097678 Jan 21 09:39 wgEncodeBroadHmmHepg2HMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5653968 Jan 21 09:39 wgEncodeBroadHmmHmecHMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5956576 Jan 21 09:39 wgEncodeBroadHmmHsmmHMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5144281 Jan 21 09:39 wgEncodeBroadHmmHuvecHMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5785441 Jan 21 09:38 wgEncodeBroadHmmK562HMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5854057 Jan 21 09:38 wgEncodeBroadHmmNhekHMM.bed.gz -rw-rw-r-- 1 encodeteam protein 5970587 Jan 21 09:38 wgEncodeBroadHmmNhlfHMM.bed.gz edit trackDb.ra template and place it in trackDb/human/hg18/wgEncodeBroadHmm cd trackDb/ make DBS=hg18 # see them there # now metadata cd {pip}/3446 mdbUpdate hg18 out/mdb.txt # Check in changes: cd .. {hg18/metaDb/alpha} mdbPrint hg18 -vars="composite=wgEncodeBroadHmm" > wgEncodeBroadHmm.ra Using table named 'hg18.metaDb_tdreszer'. objects:9 vars:135 gadd wgEncodeBroadHmm.ra cd ../../ (hg18) gadd wgEncodeBroadHmm.ra gadd trackDb.wgEncode.ra git: ci, up, push cd ../../ (trackDb) make DBS=hg18; make alpha DBS=hg18 git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg18; make alpha DBS=hg18 cd {downloadsHg18}/wgEncodeBroadHmm encodeDownloadsPage.pl -db=hg18 index.html # 9 files. No metadata # 9 found in hgFileUi #neglected to add mdb ra to make file cd .. {hg18/metaDb/alpha} e makefile git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg18; make alpha DBS=hg18 cd {downloadsHg18}/wgEncodeBroadHmm encodeDownloadsPage.pl -db=hg18 index.html # 9 files. Full metadata # 9 found in hgFileUi /cluster/data/encode/pipeline/bin/encodeStatus.pl 3446 displayed 2011-01-24 Corrections to names =============================== 12345678901234567 1 Active Promoter 2 Weak Promoter 3 Poised Promoter 4 Strong Enhancer 5 Strong Enhancer 6 Weak Enhancer 7 Weak Enhancer 8 Insulator 9 Txn Transition 10 Txn Elongation 11 Weak Txn 12 Repressed 13 Heterochrom/lo 14 Repetitive/CNV 15 Repetitive/CNV 1) Ideally lab resubmits proper beds 2) hardest: possibly edit bed files, then reload 3) Easiest: update tables show tables like "wgEncodeBroadHmm%"; | wgEncodeBroadHmmGm12878HMM | | wgEncodeBroadHmmH1hescHMM | | wgEncodeBroadHmmHepg2HMM | | wgEncodeBroadHmmHmecHMM | | wgEncodeBroadHmmHsmmHMM | | wgEncodeBroadHmmHuvecHMM | | wgEncodeBroadHmmK562HMM | | wgEncodeBroadHmmNhekHMM | | wgEncodeBroadHmmNhlfHMM | select distinct name from wgEncodeBroadHmmGm12878HMM order by name; select distinct name from wgEncodeBroadHmmH1hescHMM order by name; select distinct name from wgEncodeBroadHmmHepg2HMM order by name; select distinct name from wgEncodeBroadHmmHmecHMM order by name; select distinct name from wgEncodeBroadHmmHsmmHMM order by name; select distinct name from wgEncodeBroadHmmHuvecHMM order by name; select distinct name from wgEncodeBroadHmmK562HMM order by name; select distinct name from wgEncodeBroadHmmNhekHMM order by name; select distinct name from wgEncodeBroadHmmNhlfHMM order by name; # All are 1-15 as expected zcat wgEncodeBroadHmmGm12878HMM.bed.gz | wl zcat wgEncodeBroadHmmH1hescHMM.bed.gz | wl zcat wgEncodeBroadHmmHepg2HMM.bed.gz | wl zcat wgEncodeBroadHmmHmecHMM.bed.gz | wl zcat wgEncodeBroadHmmHsmmHMM.bed.gz | wl zcat wgEncodeBroadHmmHuvecHMM.bed.gz | wl zcat wgEncodeBroadHmmK562HMM.bed.gz | wl zcat wgEncodeBroadHmmNhekHMM.bed.gz | wl zcat wgEncodeBroadHmmNhlfHMM.bed.gz | wl zcat wgEncodeBroadHmmGm12878HMM.bed.gz | wl 570580 zcat wgEncodeBroadHmmH1hescHMM.bed.gz | wl 618287 zcat wgEncodeBroadHmmHepg2HMM.bed.gz | wl 545647 zcat wgEncodeBroadHmmHmecHMM.bed.gz | wl 608568 zcat wgEncodeBroadHmmHsmmHMM.bed.gz | wl 638307 zcat wgEncodeBroadHmmHuvecHMM.bed.gz | wl 549178 zcat wgEncodeBroadHmmK562HMM.bed.gz | wl 621678 zcat wgEncodeBroadHmmNhekHMM.bed.gz | wl 627623 zcat wgEncodeBroadHmmNhlfHMM.bed.gz | wl 640298 # Could zcat wgEncodeBroadHmmNhlfHMM.bed.gz | h | grep -P "\t10\t0\t\." > wgEncodeBroadHmmNhlfHMM.bed.1 # Could zcat wgEncodeBroadHmmNhlfHMM.bed.gz | h | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' rm wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed rm wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed rm wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed rm wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed rm wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed rm wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed rm wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed rm wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed rm wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed wl *.bed 570580 wgEncodeBroadHmmGm12878HMM.bed 618287 wgEncodeBroadHmmH1hescHMM.bed 545647 wgEncodeBroadHmmHepg2HMM.bed 608568 wgEncodeBroadHmmHmecHMM.bed 638307 wgEncodeBroadHmmHsmmHMM.bed 549178 wgEncodeBroadHmmHuvecHMM.bed 621678 wgEncodeBroadHmmK562HMM.bed 627623 wgEncodeBroadHmmNhekHMM.bed 640298 wgEncodeBroadHmmNhlfHMM.bed All okay mkdir obsolete mv wgEncodeBroadHmmGm12878HMM.bed.gz obsolete mv wgEncodeBroadHmmH1hescHMM.bed.gz obsolete mv wgEncodeBroadHmmHepg2HMM.bed.gz obsolete mv wgEncodeBroadHmmHmecHMM.bed.gz obsolete mv wgEncodeBroadHmmHsmmHMM.bed.gz obsolete mv wgEncodeBroadHmmHuvecHMM.bed.gz obsolete mv wgEncodeBroadHmmK562HMM.bed.gz obsolete mv wgEncodeBroadHmmNhekHMM.bed.gz obsolete mv wgEncodeBroadHmmNhlfHMM.bed.gz obsolete sort < wgEncodeBroadHmmGm12878HMM.bed > s_wgEncodeBroadHmmGm12878HMM.bed sort < wgEncodeBroadHmmH1hescHMM.bed > s_wgEncodeBroadHmmH1hescHMM.bed sort < wgEncodeBroadHmmHepg2HMM.bed > s_wgEncodeBroadHmmHepg2HMM.bed sort < wgEncodeBroadHmmHmecHMM.bed > s_wgEncodeBroadHmmHmecHMM.bed sort < wgEncodeBroadHmmHsmmHMM.bed > s_wgEncodeBroadHmmHsmmHMM.bed sort < wgEncodeBroadHmmHuvecHMM.bed > s_wgEncodeBroadHmmHuvecHMM.bed sort < wgEncodeBroadHmmK562HMM.bed > s_wgEncodeBroadHmmK562HMM.bed sort < wgEncodeBroadHmmNhekHMM.bed > s_wgEncodeBroadHmmNhekHMM.bed sort < wgEncodeBroadHmmNhlfHMM.bed > s_wgEncodeBroadHmmNhlfHMM.bed mv s_wgEncodeBroadHmmGm12878HMM.bed wgEncodeBroadHmmGm12878HMM.bed mv s_wgEncodeBroadHmmH1hescHMM.bed wgEncodeBroadHmmH1hescHMM.bed mv s_wgEncodeBroadHmmHepg2HMM.bed wgEncodeBroadHmmHepg2HMM.bed mv s_wgEncodeBroadHmmHmecHMM.bed wgEncodeBroadHmmHmecHMM.bed mv s_wgEncodeBroadHmmHsmmHMM.bed wgEncodeBroadHmmHsmmHMM.bed mv s_wgEncodeBroadHmmHuvecHMM.bed wgEncodeBroadHmmHuvecHMM.bed mv s_wgEncodeBroadHmmK562HMM.bed wgEncodeBroadHmmK562HMM.bed mv s_wgEncodeBroadHmmNhekHMM.bed wgEncodeBroadHmmNhekHMM.bed mv s_wgEncodeBroadHmmNhlfHMM.bed wgEncodeBroadHmmNhlfHMM.bed wl *.bed 570580 wgEncodeBroadHmmGm12878HMM.bed 618287 wgEncodeBroadHmmH1hescHMM.bed 545647 wgEncodeBroadHmmHepg2HMM.bed 608568 wgEncodeBroadHmmHmecHMM.bed 638307 wgEncodeBroadHmmHsmmHMM.bed 549178 wgEncodeBroadHmmHuvecHMM.bed 621678 wgEncodeBroadHmmK562HMM.bed 627623 wgEncodeBroadHmmNhekHMM.bed 640298 wgEncodeBroadHmmNhlfHMM.bed All okay /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmGm12878HMM_tmp wgEncodeBroadHmmGm12878HMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmH1hescHMM_tmp wgEncodeBroadHmmH1hescHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHepg2HMM_tmp wgEncodeBroadHmmHepg2HMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHmecHMM_tmp wgEncodeBroadHmmHmecHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHsmmHMM_tmp wgEncodeBroadHmmHsmmHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHuvecHMM_tmp wgEncodeBroadHmmHuvecHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmK562HMM_tmp wgEncodeBroadHmmK562HMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmNhekHMM_tmp wgEncodeBroadHmmNhekHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 /cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmNhlfHMM_tmp wgEncodeBroadHmmNhlfHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 select count(*) from wgEncodeBroadHmmGm12878HMM_tmp;| 570580 | select count(*) from wgEncodeBroadHmmH1hescHMM_tmp; | 618287 | select count(*) from wgEncodeBroadHmmHepg2HMM_tmp; | 545647 | select count(*) from wgEncodeBroadHmmHmecHMM_tmp; | 608568 | select count(*) from wgEncodeBroadHmmHsmmHMM_tmp; | 638307 | select count(*) from wgEncodeBroadHmmHuvecHMM_tmp; | 549178 | select count(*) from wgEncodeBroadHmmK562HMM_tmp; | 621678 | select count(*) from wgEncodeBroadHmmNhekHMM_tmp; | 627623 | select count(*) from wgEncodeBroadHmmNhlfHMM_tmp; | 640298 | select * from wgEncodeBroadHmmGm12878HMM_tmp limit 1;| 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmH1hescHMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmHepg2HMM_tmp limit 1; | 585 | chr1 | 0 | 400 | 15 Repetitive/CNV | 0 | . | 0 | 400 | 16777215 | select * from wgEncodeBroadHmmHmecHMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmHsmmHMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmHuvecHMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmK562HMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmNhekHMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | select * from wgEncodeBroadHmmNhlfHMM_tmp limit 1; | 585 | chr1 | 0 | 600 | 15 Repetitive/CNV | 0 | . | 0 | 600 | 16777215 | drop table wgEncodeBroadHmmGm12878HMM; drop table wgEncodeBroadHmmH1hescHMM; drop table wgEncodeBroadHmmHepg2HMM; drop table wgEncodeBroadHmmHmecHMM; drop table wgEncodeBroadHmmHsmmHMM; drop table wgEncodeBroadHmmHuvecHMM; drop table wgEncodeBroadHmmK562HMM; drop table wgEncodeBroadHmmNhekHMM; drop table wgEncodeBroadHmmNhlfHMM; rename table wgEncodeBroadHmmGm12878HMM_tmp to wgEncodeBroadHmmGm12878HMM; rename table wgEncodeBroadHmmH1hescHMM_tmp to wgEncodeBroadHmmH1hescHMM; rename table wgEncodeBroadHmmHepg2HMM_tmp to wgEncodeBroadHmmHepg2HMM; rename table wgEncodeBroadHmmHmecHMM_tmp to wgEncodeBroadHmmHmecHMM; rename table wgEncodeBroadHmmHsmmHMM_tmp to wgEncodeBroadHmmHsmmHMM; rename table wgEncodeBroadHmmHuvecHMM_tmp to wgEncodeBroadHmmHuvecHMM; rename table wgEncodeBroadHmmK562HMM_tmp to wgEncodeBroadHmmK562HMM; rename table wgEncodeBroadHmmNhekHMM_tmp to wgEncodeBroadHmmNhekHMM; rename table wgEncodeBroadHmmNhlfHMM_tmp to wgEncodeBroadHmmNhlfHMM; show tables like "wgEncodeBroadHmm%"; | wgEncodeBroadHmmGm12878HMM | | wgEncodeBroadHmmH1hescHMM | | wgEncodeBroadHmmHepg2HMM | | wgEncodeBroadHmmHmecHMM | | wgEncodeBroadHmmHsmmHMM | | wgEncodeBroadHmmHuvecHMM | | wgEncodeBroadHmmK562HMM | | wgEncodeBroadHmmNhekHMM | | wgEncodeBroadHmmNhlfHMM | select count(*) from wgEncodeBroadHmmGm12878HMM;| 570580 | select count(*) from wgEncodeBroadHmmH1hescHMM; | 618287 | select count(*) from wgEncodeBroadHmmHepg2HMM; | 545647 | select count(*) from wgEncodeBroadHmmHmecHMM; | 608568 | select count(*) from wgEncodeBroadHmmHsmmHMM; | 638307 | select count(*) from wgEncodeBroadHmmHuvecHMM; | 549178 | select count(*) from wgEncodeBroadHmmK562HMM; | 621678 | select count(*) from wgEncodeBroadHmmNhekHMM; | 627623 | select count(*) from wgEncodeBroadHmmNhlfHMM; | 640298 | gzip wgEncodeBroadHmmGm12878HMM.bed gzip wgEncodeBroadHmmH1hescHMM.bed gzip wgEncodeBroadHmmHepg2HMM.bed gzip wgEncodeBroadHmmHmecHMM.bed gzip wgEncodeBroadHmmHsmmHMM.bed gzip wgEncodeBroadHmmHuvecHMM.bed gzip wgEncodeBroadHmmK562HMM.bed gzip wgEncodeBroadHmmNhekHMM.bed gzip wgEncodeBroadHmmNhlfHMM.bed # looks good in browser # files are okay 2011-01-31 Swap out bigWigs that Brian update to version 4 ========================================================== cd /hive/users/braney/bigWigConvert.wgEncodeBroadHistone ls -1 *.bigWig | wl 151 cd {downLoads}/wgEncodeBroadHistone ls -1 *.bigWig | wl 151 mv *.bigWig ../obsolete/wgEncodeBroadHistone cd /hive/users/braney/bigWigConvert.wgEncodeBroadHistone mv wgEncodeBroadHistoneGm12878ControlStdSig.bigWig.new.bigWig /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig mv wgEncodeBroadHistoneGm12878CtcfStdSig.bigWig.new.bigWig /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878CtcfStdSig.bigWig mv wgEncodeBroadHistoneGm12878H2azStdSig.bigWig.new.bigWig /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H2azStdSig.bigWig mv wgEncodeBroadHistoneGm12878H3k27acStdSig.bigWig.new.bigWig /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27acStdSig.bigWig mv wgEncodeBroadHistoneGm12878H3k27me3StdSig.bigWig.new.bigWig /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdSig.bigWig mv wgEncodeBroadHistoneGm12878H3k36me3StdSig.bigWig.new.bigWig /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k36me3StdSig.bigWig ... cd {downLoads}/wgEncodeBroadHistone ls -1 *.bigWig | wl 151 cd release1/ ls -1 *.bigWig | wl 151 # These are links to obsolete bigWigs rm *.bigWig ls ../*.bigWig . ls -1 *.bigWig | wl 151 # Check that bigWigs work in browser. This will check that /gbdb/hg19/bbi link is okay too AOKAY # check metadata by building index.html ../ encodeDownloadsPage.pl -db=hg19 index.html 1251 files all with metadata. # 1251 file in hgFileUi too encodeDownloadsPage.pl -db=hg19 -checksum index.html & 2011-02-07 Change white items to ?? =================================== Currently: 1 255,0,0 #FF0000 2 255,105,105 #FF6969 3 207,11,198 #CF0BC6 4 250,202,0 #FACA00 5 250,202,0 #FACA00 6 255,252,4 #FFFC04 7 255,252,4 #FFFC04 8 10,190,254 #0ABEFE 704254 9 0,176,80 #00B050 10 0,176,80 #00B050 11 153,255,102 #99FF66 12 127,127,127 #7F7F7F 13 255,255,255 #FFFFFF => #F5F5F5 16119285 14 255,255,255 #FFFFFF => #D3D3D3 13882323 15 255,255,255 #FFFFFF => #DCDCDC 14474460 select count(*) from wgEncodeBroadHmmNhlfHMM where reserved = 16777215;| 103835 | update wgEncodeBroadHmmGm12878HMM set reserved = 16119285 where reserved = 16777215; Rows matched: 88467 Changed: 88467 Warnings: 0 update wgEncodeBroadHmmH1hescHMM set reserved = 16119285 where reserved = 16777215; Rows matched: 96621 Changed: 96621 Warnings: 0 update wgEncodeBroadHmmHepg2HMM set reserved = 16119285 where reserved = 16777215; Rows matched: 84990 Changed: 84990 Warnings: 0 update wgEncodeBroadHmmHmecHMM set reserved = 16119285 where reserved = 16777215; Rows matched: 90848 Changed: 90848 Warnings: 0 update wgEncodeBroadHmmHsmmHMM set reserved = 16119285 where reserved = 16777215; Rows matched: 87160 Changed: 87160 Warnings: 0 update wgEncodeBroadHmmHuvecHMM set reserved = 16119285 where reserved = 16777215; Rows matched: 90766 Changed: 90766 Warnings: 0 update wgEncodeBroadHmmK562HMM set reserved = 16119285 where reserved = 16777215; Rows matched: 93219 Changed: 93219 Warnings: 0 update wgEncodeBroadHmmNhekHMM set reserved = 16119285 where reserved = 16777215; Rows matched: 92707 Changed: 92707 Warnings: 0 update wgEncodeBroadHmmNhlfHMM set reserved = 16119285 where reserved = 16777215; Rows matched: 103835 Changed: 103835 Warnings: 0 2011-02-10 Preparing for Release of HMM ======================================= Got description and added them. ## No restrictions on this data so will remove this setting. select * from metaDb_tdreszer where obj like "WgEncodeBroadHmm%" and var = "dateUnrestricted"; | wgEncodeBroadHmmGm12878HMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmH1hescHMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmHepg2HMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmHmecHMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmHsmmHMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmHuvecHMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmK562HMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmNhekHMM | dateUnrestricted | txt | 2011-10-21 | | wgEncodeBroadHmmNhlfHMM | dateUnrestricted | txt | 2011-10-21 | update metaDb_tdreszer set val = "2011-01-21" where obj like "WgEncodeBroadHmm%" and var = "dateUnrestricted"; # date submitted # Perhaps could remove this, but I don't want any unexpected stuff happening. I found that the calculated date shows up in hgTrackUi! cd (downloads)/wgEncodeBroadHmm encodeDownloadsPage.pl -checksum index.html mkdir release1 cd release1/ cp ../index.html . cp ../files.txt . cp ../md5sum.txt . ln ../*.gz . ll ../ | grep -v \.gz$ | grep -v \.html | grep -v \.txt # Nothing missing ls -1 | wl 12 # expect 9 + 3 = 12 cd .. ~/bin/scripts/encodeMkChangeNotes hg18 release1 - > release1/wgEncodeBroadHmm.release1.notes cp release1/wgEncodeBroadHmm.release1.notes ~/kent/src/hg/makeDb/doc/encodeDccHg18/ /cluster/data/encode/pipeline/bin/encodeStatus.pl 3446 approved # to be done: /cluster/data/encode/pipeline/bin/encodeStatus.pl 3446 reviewing 2011-04-20 Experimentify ======================== cd trackDb/human/hg18/metaDb/alpha mdbPrint hg18 -composite=%BroadCh% -experimentify > tmp.txt mdbUpdate hg18 -composite=%BroadCh% -encodeExp=std -test Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadChipSeq' has 93 recognizable experiments with 0 missing an expId. objects/experiment: min:5 max:6 mean:5.903226. Found 549 of 550 object(s) would have their experiment ID updated. mdbUpdate hg18 -composite=%BroadCh% -encodeExp=std Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadHistone' has 93 recognizable experiments with 93 missing an expId. objects/experiment: min:3 max:8 mean:6.158940. Affected 549 row(s) in hg18.metaDb_tdreszer mdbUpdate hg18 -composite=%BroadCh% -encodeExp=std -accession Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadChipSeq' has 93 recognizable experiments with 0 missing an expId. objects/experiment: min:5 max:6 mean:5.903226. Affected 549 row(s) in hg18.metaDb_tdreszer mdbPrint hg18 -composite=wgEncodeBroadChipSeq > wgEncodeBroadChipSeq.ra Using table named 'hg18.metaDb_tdreszer'. objects:550 vars:11162 gold, gadd, gci, gup,gpush mdbPrint hg18 -composite=%BroadHmm -experimentify > tmp.txt Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. objects:10 vars:138 mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std -test Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 9 missing an expId. objects/experiment: min:1 max:1 mean:1.000000. Found 9 of 10 object(s) would have their experiment ID updated. Command would affected 9 row(s) in hg18.metaDb_tdreszer mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 9 missing an expId. objects/experiment: min:1 max:1 mean:1.000000. Affected 9 row(s) in hg18.metaDb_tdreszer mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std -accession -test Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 0 missing an expId. objects/experiment: min:1 max:1 mean:1.000000. Found 9 of 10 object(s) would have their experiment ID updated. Command would affected 9 row(s) in hg18.metaDb_tdreszer mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std -accession Using hgFixed.encodeExp Using table named 'hg18.metaDb_tdreszer'. Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 0 missing an expId. objects/experiment: min:1 max:1 mean:1.000000. Affected 9 row(s) in hg18.metaDb_tdreszer mdbPrint hg18 -composite=wgEncodeBroadHmm > wgEncodeBroadHmm.ra Using table named 'hg18.metaDb_tdreszer'. objects:10 vars:156 gold wgEncodeBroadHmm.ra gold, gadd, gci, gup,gpush cd {downloads}/wgEncodeBroadChipSeq encodeDownloadsPage.pl -db=hg18 index.html cd {downloads}/wgEncodeBroadHmm encodeDownloadsPage.pl -db=hg18 index.html cp index.html release1/ cp files.txt release1/