File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/ctl1/ENCFF000YRB.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/ctl1/ENCFF000YRB.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/ctl1/ENCFF000YRB.merged.nodup.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep1/pseudorep1/ENCFF000YEU.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep1/pseudorep2/ENCFF000YEU.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep1/ENCFF000YEU.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep1/ENCFF000YEU.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep1/ENCFF000YEU.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep2/pseudorep1/ENCFF000YEW.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep2/pseudorep2/ENCFF000YEW.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep2/ENCFF000YEW.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep2/ENCFF000YEW.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFY/align/rep2/ENCFF000YEW.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.gz
Pooled replicate
Pseudoreplicate 1
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.gz
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep1/ENCFF000YEU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep1/ENCFF000YEU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep1/ENCFF000YEU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep1/ENCFF000YEU.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep2/ENCFF000YEU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep2/ENCFF000YEU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep2/ENCFF000YEU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/pseudorep2/ENCFF000YEU.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.300K.regionPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep1/ENCFF000YEW.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep1/ENCFF000YEW.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep1/ENCFF000YEW.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep1/ENCFF000YEW.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep2/ENCFF000YEW.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep2/ENCFF000YEW.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep2/ENCFF000YEW.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/pseudorep2/ENCFF000YEW.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFY/peak/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/ctl1/ENCFF000YRB.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/ctl1/ENCFF000YRB.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/ctl1/ENCFF000YRB.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/ctl1/ENCFF000YRB.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.png
Pooled replicate
Pseudoreplicate 1
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.frip.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.png
Replicate 1
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/pseudorep1/ENCFF000YEU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/pseudorep2/ENCFF000YEU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep1/ENCFF000YEU.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/pseudorep1/ENCFF000YEW.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/pseudorep2/ENCFF000YEW.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/rep2/ENCFF000YEW.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/ENCFF000YEU.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000EFY/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFY/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFY/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFY/signal/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFY/signal/rep1/ENCFF000YEU.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFY/signal/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFY/signal/rep2/ENCFF000YEW.merged.nodup_x_ctl_for_rep2.pval.signal.bigwig
Task graph D cluster_pooled_rep Pooled replicate cluster_rep1 Replicate 1 cluster_rep2 Replicate 2 cluster_ctl1 Control 1 -2179597008397319952 chip.macs2_signal_track_pooled 852280414664734863 BW FC -2179597008397319952->852280414664734863 -2119446934364373310 BW p-val -2179597008397319952->-2119446934364373310 7079134515219216462 chip.call_peak_pooled 7197458067640756963 Peak (bfilt) 7079134515219216462->7197458067640756963 345693861557151262 Peak 7079134515219216462->345693861557151262 -6337497924917819313 chip.idr_ppr 345693861557151262->-6337497924917819313 391033055477843059 chip.idr 345693861557151262->391033055477843059 -5796216353827198831 chip.overlap 345693861557151262->-5796216353827198831 8323955749518521606 chip.overlap_ppr 345693861557151262->8323955749518521606 222741910539493394 chip.pool_ta 2113781739924784829 TAG-ALIGN 222741910539493394->2113781739924784829 2113781739924784829->-2179597008397319952 2113781739924784829->7079134515219216462 5144337574282850075 chip.call_peak 2113781739924784829->5144337574282850075 5276422345005056480 chip.macs2_signal_track 2113781739924784829->5276422345005056480 -9018527887191627006 chip.call_peak 2113781739924784829->-9018527887191627006 -8099053200105194139 chip.macs2_signal_track 2113781739924784829->-8099053200105194139 2113781739924784829->-6337497924917819313 2113781739924784829->391033055477843059 2113781739924784829->-5796216353827198831 8838259626584966020 chip.reproducibility_overlap 2113781739924784829->8838259626584966020 -2077625184389724772 chip.reproducibility_idr 2113781739924784829->-2077625184389724772 2113781739924784829->8323955749518521606 5545888638847367134 Peak (bfilt) 5144337574282850075->5545888638847367134 4917780952405063776 Peak 5144337574282850075->4917780952405063776 4917780952405063776->391033055477843059 4917780952405063776->-5796216353827198831 4917780952405063776->8838259626584966020 4917780952405063776->-2077625184389724772 -8075405265276579387 chip.bam2ta -406545366293890184 TAG-ALIGN -8075405265276579387->-406545366293890184 -406545366293890184->222741910539493394 -406545366293890184->5144337574282850075 -406545366293890184->5276422345005056480 -406545366293890184->-9018527887191627006 -406545366293890184->-8099053200105194139 -406545366293890184->-6337497924917819313 -406545366293890184->8838259626584966020 -406545366293890184->-2077625184389724772 -406545366293890184->8323955749518521606 2189211811935941210 chip.filter -4489669976540058758 SAMstats QC 2189211811935941210->-4489669976540058758 -7223659788105075281 Filt/deduped BAM 2189211811935941210->-7223659788105075281 -3453946657118450744 LibCmplx QC 2189211811935941210->-3453946657118450744 -7223659788105075281->-8075405265276579387 8119471719161557540 chip.jsd -7223659788105075281->8119471719161557540 -4324182627518024677 chip.align 7716473720550097323 SAMstats QC -4324182627518024677->7716473720550097323 -5443932546482969057 BAM -4324182627518024677->-5443932546482969057 -5443932546482969057->2189211811935941210 -496325521646928194 chip.xcor 4973354581402548325 XCOR Plot -496325521646928194->4973354581402548325 -8530287726886953324 BW FC 5276422345005056480->-8530287726886953324 9151779834977342611 BW p-val 5276422345005056480->9151779834977342611 1997507474665764241 FASTQ R1 (1) 1997507474665764241->-4324182627518024677 1997507474665764241->-496325521646928194 6040385831215482808 Peak (bfilt) -9018527887191627006->6040385831215482808 7068929862454758179 Peak -9018527887191627006->7068929862454758179 7068929862454758179->391033055477843059 7068929862454758179->-5796216353827198831 7068929862454758179->8838259626584966020 7068929862454758179->-2077625184389724772 2036957869264920661 chip.bam2ta 7891780685401868866 TAG-ALIGN 2036957869264920661->7891780685401868866 7891780685401868866->222741910539493394 7891780685401868866->5144337574282850075 7891780685401868866->5276422345005056480 7891780685401868866->-9018527887191627006 7891780685401868866->-8099053200105194139 7891780685401868866->-6337497924917819313 7891780685401868866->8838259626584966020 7891780685401868866->-2077625184389724772 7891780685401868866->8323955749518521606 -8399874734173307819 chip.filter -4000292814419757440 SAMstats QC -8399874734173307819->-4000292814419757440 -7298983869274607418 Filt/deduped BAM -8399874734173307819->-7298983869274607418 -2856339902166153000 LibCmplx QC -8399874734173307819->-2856339902166153000 -7298983869274607418->2036957869264920661 -7298983869274607418->8119471719161557540 6388807927931493871 chip.align 532433520334815962 BAM 6388807927931493871->532433520334815962 9222477456509234125 SAMstats QC 6388807927931493871->9222477456509234125 532433520334815962->-8399874734173307819 5934771502979358981 chip.xcor 4681339760891981634 XCOR Plot 5934771502979358981->4681339760891981634 -4880022504369114596 BW FC -8099053200105194139->-4880022504369114596 -9049801980748442212 BW p-val -8099053200105194139->-9049801980748442212 2751184158247209691 FASTQ R1 (1) 2751184158247209691->6388807927931493871 2751184158247209691->5934771502979358981 8823083733449991554 chip.bam2ta_ctl -3056435293862005989 TAG-ALIGN 8823083733449991554->-3056435293862005989 -3056435293862005989->-2179597008397319952 -3056435293862005989->7079134515219216462 -3056435293862005989->5144337574282850075 -3056435293862005989->5276422345005056480 -3056435293862005989->-9018527887191627006 -3056435293862005989->-8099053200105194139 -3056435293862005989->-6337497924917819313 -3056435293862005989->8838259626584966020 -3056435293862005989->-2077625184389724772 -3056435293862005989->8323955749518521606 -6324747490512112888 chip.filter_ctl -2210361162529854204 SAMstats QC -6324747490512112888->-2210361162529854204 6345032826536080548 Filt/deduped BAM -6324747490512112888->6345032826536080548 -7259754542221046158 LibCmplx QC -6324747490512112888->-7259754542221046158 6345032826536080548->8823083733449991554 6345032826536080548->8119471719161557540 2014661521926738728 chip.align_ctl -1307344367108031159 SAMstats QC 2014661521926738728->-1307344367108031159 556223341982627599 BAM 2014661521926738728->556223341982627599 556223341982627599->-6324747490512112888 680334703620741862 FASTQ R1 (1) 680334703620741862->2014661521926738728 5418758797145043732 IDR Plot ppr -6337497924917819313->5418758797145043732 2665914236495860940 IDR Peak ppr -6337497924917819313->2665914236495860940 2665914236495860940->-2077625184389724772 7733763331026638363 IDR Plot rep1_vs_rep2 391033055477843059->7733763331026638363 -4434331786819736753 IDR NPeak rep1_vs_rep2 391033055477843059->-4434331786819736753 -4434331786819736753->-2077625184389724772 8402722055672291233 Overlap Peak rep1_vs_rep2 -5796216353827198831->8402722055672291233 8402722055672291233->8838259626584966020 4305624873077943299 Overlap Peak optimal 8838259626584966020->4305624873077943299 -6961458264642436396 Overlap reproducibility 8838259626584966020->-6961458264642436396 9189259023838152910 IDR Peak optimal -2077625184389724772->9189259023838152910 9027160296976979186 IDR reproducibility -2077625184389724772->9027160296976979186 -1807821859391170069 Overlap Peak ppr 8323955749518521606->-1807821859391170069 -1807821859391170069->8838259626584966020 -5208979782810329531 JSD Plot 8119471719161557540->-5208979782810329531

UCSC browser tracks

UCSC track hub plain text 
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