## 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 view for coverage and junction tracks track hoffmanRnaseqSiBrg1Set compositeTrack on shortLabel Hoffman siBrg1 RNAseq longLabel Hoffman siBrg1 RNAseq priority 830 #visibility full subGroup1 view Views \ COV=Coverage \ JUNC=Junction subGroup2 treatment Treatment \ siBrg1=siBrg1 \ Control=Control subGroup3 content Data_Content \ REP=Replicates \ UNION=Union dimensions dimX=treatment dimY=content sortOrder treatment=+ content=+ view=+ type bed 3 configurable on ## Views track for siBrg1 RNAseq, coverage data track hoffmanRnaseqSiBrg1View1 parent hoffmanRnaseqSiBrg1Set shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 viewUi on ## RNAseq data coverage tracks ## siBrg1 replicate 1 track siBrg1_r1 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES638_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r1 longLabel RNAseq siBrg1_r1 type bigWig color 176,32,36 priority 831 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=REP view=COV ## siBrg1 replicate 2 track siBrg1_r2 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES639_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r2 longLabel RNAseq siBrg1_r2 type bigWig color 176,32,36 priority 832 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=REP view=COV ## siBrg1 replicate 3 track siBrg1_r3 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES640_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r3 longLabel RNAseq siBrg1_r3 type bigWig color 176,32,36 priority 833 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=REP view=COV ## Control replicate 1 track Control_r1 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES641_merged.topHat2pe.bw shortLabel RNAseq Control_r1 longLabel RNAseq Control_r1 type bigWig color 110,110,140 priority 835 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=Control content=REP view=COV ## Control replicate 2 track Control_r2 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES642_merged.topHat2pe.bw shortLabel RNAseq Control_r2 longLabel RNAseq Control_r2 type bigWig color 110,110,140 priority 836 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=Control content=REP view=COV ## Control replicate 3 track Control_r3 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES643_merged.topHat2pe.bw shortLabel RNAseq Control_r3 longLabel RNAseq Control_r3 type bigWig color 110,110,140 priority 837 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=Control content=REP view=COV # Union of coverages across replicates per sample group ## RNAseq data coverage track union ## siBrg1 union coverage track siBrg1_union parent hoffmanRnaseqSiBrg1View1 on bigDataUrl siBrg1_union.TopHat2pe.bw shortLabel RNAseq siBrg1 longLabel RNAseq siBrg1 type bigWig color 146,22,24 priority 830 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=UNION view=COV ## Control union coverage track Control_union parent hoffmanRnaseqSiBrg1View1 on bigDataUrl Control_union.TopHat2pe.bw shortLabel RNAseq Control longLabel RNAseq Control type bigWig color 90,90,110 priority 834 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full subGroups treatment=Control content=UNION view=COV ## Views track for siBrg1 RNAseq, coverage data track hoffmanRnaseqSiBrg1View2 parent hoffmanRnaseqSiBrg1Set shortLabel RNAseq_junctions view JUNC visibility pack type bigBed 12 allButtonPair on centerLabelsDense on dragAndDrop on thickDrawItem on scoreFilter 10 scoreFilterLimits 1:1000 viewUi on # siBrg1_r1 junctions track siBrg1_r1_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES638_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r1 longLabel TopHat2 junctions siBrg1_r1 type bigBed 12 color 176,32,36 visibility pack priority 851 subGroups treatment=siBrg1 content=REP view=JUNC # siBrg1_r2 junctions track siBrg1_r2_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES639_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r2 longLabel TopHat2 junctions siBrg1_r2 type bigBed 12 color 176,32,36 visibility pack priority 852 subGroups treatment=siBrg1 content=REP view=JUNC # siBrg1_r3 junctions track siBrg1_r3_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES640_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r3 longLabel TopHat2 junctions siBrg1_r3 type bigBed 12 color 176,32,36 visibility pack priority 853 subGroups treatment=siBrg1 content=REP view=JUNC # Control_r1 junctions track Control_r1_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES641_merged.junctions.bb shortLabel TopHat2 junctions Control_r1 longLabel TopHat2 junctions Control_r1 type bigBed 12 color 110,110,140 visibility pack priority 855 subGroups treatment=Control content=REP view=JUNC # Control_r2 junctions track Control_r2_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES642_merged.junctions.bb shortLabel TopHat2 junctions Control_r2 longLabel TopHat2 junctions Control_r2 type bigBed 12 color 110,110,140 visibility pack priority 856 subGroups treatment=Control content=REP view=JUNC # Control_r3 junctions track Control_r3_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES643_merged.junctions.bb shortLabel TopHat2 junctions Control_r3 longLabel TopHat2 junctions Control_r3 type bigBed 12 color 110,110,140 visibility pack priority 857 subGroups treatment=Control content=REP view=JUNC # siBrg1 combined junctions # siBrg1_combined_junctions.bb track siBrg1_junc parent hoffmanRnaseqSiBrg1View2 on bigDataUrl siBrg1_combined_junctions.bed12sort.bb shortLabel TopHat2 junctions siBrg1 longLabel TopHat2 junctions siBrg1 type bigBed 12 visibility pack priority 850 spectrum on scoreMin 10 scoreMax 100 # color 73,11,12 color 150,0,0 # altColor 201,30,33 # scoreFilter 10 # scoreFilterLimits 1:1000 # thickDrawItem on subGroups treatment=siBrg1 content=UNION view=JUNC # Control combined junctions # Control_combined_junctions.bb track Control_junc parent hoffmanRnaseqSiBrg1View2 on bigDataUrl Control_combined_junctions.bed12sort.bb shortLabel TopHat2 junctions Control longLabel TopHat2 junctions Control type bigBed 12 visibility pack priority 854 spectrum on scoreMin 10 scoreMax 100 # color 45,45,55 color 100,100,100 # altColor 149,149,183 # scoreFilter 10 # scoreFilterLimits 1:1000 # thickDrawItem on subGroups treatment=Control content=UNION view=JUNC # 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