## RNA-seq data coverage track set track hoffmanRnaseqSiBrg1Set compositeTrack on shortLabel Hoffman siBrg1 RNA-seq coverage, TopHat2 longLabel Hoffman siBrg1 RNA-seq coverage, TopHat2 type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 833 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## RNA-seq data coverage tracks ## siBrg1 replicate 1 track siBrg1_r1 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES638_merged.topHat2pe.bw shortLabel RNA-seq siBrg1_r1 longLabel RNA-seq siBrg1_r1 type bigWig color 176,32,36 priority 834 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## siBrg1 replicate 2 track siBrg1_r2 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES639_merged.topHat2pe.bw shortLabel RNA-seq siBrg1_r2 longLabel RNA-seq siBrg1_r2 type bigWig color 176,32,36 priority 836 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## siBrg1 replicate 3 track siBrg1_r3 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES640_merged.topHat2pe.bw shortLabel RNA-seq siBrg1_r3 longLabel RNA-seq siBrg1_r3 type bigWig color 176,32,36 priority 838 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## Control replicate 1 track Control_r1 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES641_merged.topHat2pe.bw shortLabel RNA-seq Control_r1 longLabel RNA-seq Control_r1 type bigWig color 110,110,140 priority 840 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## Control replicate 2 track Control_r2 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES642_merged.topHat2pe.bw shortLabel RNA-seq Control_r2 longLabel RNA-seq Control_r2 type bigWig color 110,110,140 priority 842 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## Control replicate 3 track Control_r3 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES643_merged.topHat2pe.bw shortLabel RNA-seq Control_r3 longLabel RNA-seq Control_r3 type bigWig color 110,110,140 priority 844 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## TopHat2 junctions, merged across lanes per sample track TopHat2Junc compositeTrack on shortLabel TopHat2 merged junctions longLabel TopHat2 merged junctions type bigBed 12 allButtonPair on centerLabelsDense on dragAndDrop on priority 580 visibility dense # siBrg1_r1 junctions track siBrg1_r1_junc parent TopHat2Junc bigDataUrl ES638_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r1 longLabel TopHat2 junctions siBrg1_r1 type bigBed 12 color 176,32,36 visibility dense priority 581 # siBrg1_r2 junctions track siBrg1_r2_junc parent TopHat2Junc bigDataUrl ES639_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r2 longLabel TopHat2 junctions siBrg1_r2 type bigBed 12 color 176,32,36 visibility dense priority 582 # siBrg1_r3 junctions track siBrg1_r3_junc parent TopHat2Junc bigDataUrl ES640_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r3 longLabel TopHat2 junctions siBrg1_r3 type bigBed 12 color 176,32,36 visibility dense priority 583 # Control_r1 junctions track Control_r1_junc parent TopHat2Junc bigDataUrl ES641_merged.junctions.bb shortLabel TopHat2 junctions Control_r1 longLabel TopHat2 junctions Control_r1 type bigBed 12 color 110,110,140 visibility dense priority 584 # Control_r2 junctions track Control_r2_junc parent TopHat2Junc bigDataUrl ES642_merged.junctions.bb shortLabel TopHat2 junctions Control_r2 longLabel TopHat2 junctions Control_r2 type bigBed 12 color 110,110,140 visibility dense priority 585 # Control_r3 junctions track Control_r3_junc parent TopHat2Junc bigDataUrl ES643_merged.junctions.bb shortLabel TopHat2 junctions Control_r3 longLabel TopHat2 junctions Control_r3 type bigBed 12 color 110,110,140 visibility dense priority 586 ## TopHat2 junctions, merged across lanes per sample track TopHat2JuncComb compositeTrack on shortLabel TopHat2 combined junctions longLabel TopHat2 combined junctions type bigBed 12 allButtonPair on centerLabelsDense on dragAndDrop on priority 570 visibility pack thickDrawItem on # siBrg1 combined junctions # siBrg1_combined_junctions.bb track siBrg1_junc parent TopHat2JuncComb bigDataUrl siBrg1_combined_junctions.bed12sort.bb shortLabel TopHat2 junctions siBrg1 longLabel TopHat2 junctions siBrg1 type bigBed 12 . visibility pack priority 575 spectrum on scoreMin 1 scoreMax 200 color 128,0,0 altColor 255,128,128 scoreFilterLimits 1:1000 scoreFilter 10 minGrayLevel 4 # Control combined junctions # Control_combined_junctions.bb track Control_junc parent TopHat2JuncComb bigDataUrl Control_combined_junctions.bed12sort.bb shortLabel TopHat2 junctions Control longLabel TopHat2 junctions Control type bigBed 12 . visibility pack priority 576 spectrum on scoreMin 0 scoreMax 200 color 0,0,128 altColor 128,128,255 scoreFilterLimits 1:1000 scoreFilter 10 minGrayLevel 4 # MES230_1.sanger.sickle.bowtieSe_hg19.sorted.bw ## ChIP-seq data coverage track set for MiSeq runs track hoffmanMiseqSet compositeTrack on shortLabel Hoffman Input ChIP-seq coverage longLabel Hoffman Input ChIP-seq coverage type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 933 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## RNA-seq data coverage tracks ## Input lane track Input_MiSeq parent hoffmanMiseqSet on bigDataUrl MES230_1.sanger.sickle.bowtieSe_hg19.sorted.bw shortLabel ChIP-seq Input longLabel ChIP-seq Input type bigWig color 110,110,140 priority 934 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## Brg1 ChIP lane track Brg1_MiSeq parent hoffmanMiseqSet on bigDataUrl MES231_1.sanger.sickle.bowtieSe_hg19.sorted.bw shortLabel Brg1 ChIP-seq longLabel Brg1 ChIP-seq type bigWig color 255,112,0 priority 936 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## PolII ChIP lane track PolII_MiSeq parent hoffmanMiseqSet on bigDataUrl MES232_1.sanger.sickle.bowtieSe_hg19.sorted.bw shortLabel PolII ChIP-seq longLabel PolII ChIP-seq type bigWig color 37,113,53 priority 937 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full # MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw # MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw ## ChIP-seq data coverage track set for MiSeq runs track hoffmanMiseqSet200 compositeTrack on shortLabel Hoffman Input ChIP-seq coverage longLabel Hoffman Input ChIP-seq coverage type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 953 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## RNA-seq data coverage tracks ## Input lane track Input_MiSeq200 parent hoffmanMiseqSet200 on bigDataUrl MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel ChIP-seq Input +200bp longLabel ChIP-seq Input +200bp type bigWig color 110,110,140 priority 954 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## Brg1 ChIP lane track Brg1_MiSeq200 parent hoffmanMiseqSet200 on bigDataUrl MES231_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel Brg1 ChIP-seq +200bp longLabel Brg1 ChIP-seq +200bp type bigWig color 255,112,0 priority 956 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## PolII ChIP lane track PolII_MiSeq200 parent hoffmanMiseqSet200 on bigDataUrl MES232_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel PolII ChIP-seq +200bp longLabel PolII ChIP-seq +200bp type bigWig color 37,113,53 priority 957 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## TopHat2 junctions, merged across lanes per sample track homerMiseqPeaks compositeTrack on shortLabel HOMER MiSeq Peaks longLabel HOMER MiSeq Peaks type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 680 visibility dense # RNA PolII ChIP-seq on MiSeq vs Input control track pol2chip_1k150fc4e3 parent homerMiseqPeaks bigDataUrl homerComparison_PolIIChIP_Vs_InputControl.findPeaks_histoneregion.150.1000_fdr0.001_foc0.9_loc2000_fc4_min0.sorted.bb shortLabel PolII vs Input longLabel PolII vs Input 1k150fc4e3 type bigBed color 37,113,53 visibility dense priority 681 # Brg1 ChIP-seq peaks from Miseq track Brg1chip_1k150fc4e3 parent homerMiseqPeaks bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_histoneregion.150.1000_fdr0.001_foc0.9_loc2000_fc4_min0.sorted.bb shortLabel Brg1 vs Input P.001 longLabel Brg1 vs Input 1k150fc4e3 type bigBed color 255,112,0 visibility dense priority 582 # Brg1 ChIP-seq peaks from Miseq - fc2, P-value 0.003 track Brg1chip_1k150fc2e3 parent homerMiseqPeaks bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_histoneregion.150.1000_fdr0.003_p0.003_foc0.9_loc2000_fc2_min0.sorted.bb shortLabel Brg1 vs Input P.003 longLabel Brg1 vs Input 1k150fc2e3 type bigBed color 255,112,0 visibility dense priority 583