## SuperTracks to contain the composite subgroups of tracks ## Hoffman siBrg1 RNAseq track JHsiBrg1RnaSeqSuper superTrack on show shortLabel Hoffman siBrg1 RNAseq longLabel Hoffman siBrg1 RNAseq priority 10 group hoffmanSiBrg1RNAseq ## Hoffman siBaf60a RNAseq #track JHsiBaf60aRnaSeqSuper #superTrack on show #shortLabel Hoffman siBaf60a RNAseq #longLabel Hoffman siBaf60a RNAseq #priority 20 ## Hoffman ChIPseq track JHchipSeqSuper superTrack on show shortLabel Hoffman ChIPseq longLabel Hoffman ChIPseq priority 30 group hoffmanChIPseq ## RNAseq data coverage track set track hoffmanRnaseqSiBrg1Set parent JHsiBrg1RnaSeqSuper compositeTrack on shortLabel Hoffman siBrg1 RNAseq coverage longLabel Hoffman siBrg1 RNAseq coverage 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 ## RNAseq data coverage tracks ## siBrg1 replicate 1 track siBrg1_r1 parent hoffmanRnaseqSiBrg1Set on bigDataUrl ES638_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r1 longLabel RNAseq 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 RNAseq siBrg1_r2 longLabel RNAseq 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 RNAseq siBrg1_r3 longLabel RNAseq 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 RNAseq Control_r1 longLabel RNAseq 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 RNAseq Control_r2 longLabel RNAseq 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 RNAseq Control_r3 longLabel RNAseq 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 # Union of coverages across replicates per sample group ## Union RNAseq data coverage track set track hoffmanRnaseqSiBrg1UnionSet parent JHsiBrg1RnaSeqSuper compositeTrack on shortLabel Hoffman siBrg1 RNAseq coverage union longLabel Hoffman siBrg1 RNAseq coverage union type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 823 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full ## RNAseq data coverage tracks ## siBrg1 union coverage track siBrg1_union parent hoffmanRnaseqSiBrg1UnionSet on bigDataUrl siBrg1_union.TopHat2pe.bw shortLabel RNAseq siBrg1_union longLabel RNAseq siBrg1_union type bigWig color 146,22,24 priority 854 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full ## Control union coverage track Control_union parent hoffmanRnaseqSiBrg1UnionSet on bigDataUrl Control_union.TopHat2pe.bw shortLabel RNAseq Control_union longLabel RNAseq Control_union type bigWig color 90,90,110 priority 855 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full ## TopHat2 junctions, merged across lanes per sample track TopHat2Junc parent JHsiBrg1RnaSeqSuper compositeTrack hide shortLabel TopHat2 junctions longLabel TopHat2 junctions type bigBed 12 allButtonPair on centerLabelsDense on dragAndDrop on priority 580 visibility hide # 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 parent JHsiBrg1RnaSeqSuper compositeTrack on shortLabel TopHat2 junctions union longLabel TopHat2 junctions union 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 color 146,22,24 #color 128,0,0 scoreFilter 10 scoreFilterLimits 1:1000 # 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 color 90,90,110 #color 0,0,128 scoreFilter 10 scoreFilterLimits 1:1000 # MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw ## ChIPseq data coverage track set for MiSeq runs track hoffmanMiseqSet200 parent JHchipSeqSuper compositeTrack hide shortLabel Hoffman ChIPseq coverage longLabel Hoffman ChIPseq 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 hide ## RNAseq data coverage tracks ## Input lane track Input_MiSeq200 parent hoffmanMiseqSet200 on bigDataUrl MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel ChIPseq Input +200bp longLabel ChIPseq 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 ChIPseq +200bp longLabel Brg1 ChIPseq +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 ChIPseq +200bp longLabel PolII ChIPseq +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 ## HOMER MiSeq Peaks track homerMiseqPeaks parent JHchipSeqSuper compositeTrack on shortLabel HOMER MiSeq Peaks longLabel HOMER MiSeq Peaks type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 680 visibility hide # RNA PolII ChIPseq 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 ChIPseq 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 ChIPseq 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 # MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw ## ChIPseq data coverage track set for MiSeq runs track hoffmanMiseqSet200_dec2013 parent JHchipSeqSuper compositeTrack on shortLabel Hoffman ChIPseq coverage union longLabel Hoffman ChIPseq coverage union type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 973 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## ChIPseq data coverage tracks union ## Input lane track Input_MiSeq200_dec2013 parent hoffmanMiseqSet200_dec2013 on bigDataUrl InputControl_s.sickle.merged.bowtieSe_hg19.sorted.slop200.bw shortLabel ChIPseq Input union longLabel ChIPseq Input union type bigWig color 110,110,140 priority 974 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_dec2013 parent hoffmanMiseqSet200_dec2013 on bigDataUrl Brg1ChIP_s.sickle.merged.bowtieSe_hg19.sorted.slop200.bw shortLabel Brg1 ChIPseq union longLabel Brg1 ChIPseq union type bigWig color 255,112,0 priority 976 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_dec2013 parent hoffmanMiseqSet200_dec2013 on bigDataUrl PolIIChIP_s.sickle.merged.bowtieSe_hg19.sorted.slop200.bw shortLabel PolII ChIPseq union longLabel PolII ChIPseq union type bigWig color 37,113,53 priority 977 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full ## HOMER MiSeq ChIPseq peaks using union coverage data, minimum tags per peak track homerMiseqPeaks_jan2014 parent JHchipSeqSuper compositeTrack on shortLabel HOMER MiSeq Peaks union longLabel HOMER MiSeq Peaks union type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 690 visibility dense # RNA PolII ChIPseq on MiSeq vs Input control track pol2chip_jan2014_min10 parent homerMiseqPeaks_jan2014 bigDataUrl homerComparison_PolIIChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min10.sorted.bb shortLabel PolII vs Input union min10 longLabel PolII vs Input union min10 type bigBed color 37,113,53 visibility dense priority 691 track pol2chip_jan2014_min5 parent homerMiseqPeaks_jan2014 bigDataUrl homerComparison_PolIIChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min5.sorted.bb shortLabel PolII vs Input union min5 longLabel PolII vs Input union min5 type bigBed color 37,113,53 visibility hide priority 692 # Brg1 ChIPseq peaks from Miseq track Brg1chip_jan2014_min10 parent homerMiseqPeaks_jan2014 bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min10.sorted.bb shortLabel Brg1 vs Input union min10 longLabel Brg1 vs Input union min10 type bigBed color 255,112,0 visibility dense priority 695 track Brg1chip_jan2014_min5 parent homerMiseqPeaks_jan2014 bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min5.sorted.bb shortLabel Brg1 vs Input union min5 longLabel Brg1 vs Input union min5 type bigBed color 255,112,0 visibility hide priority 696