File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/ctl1/ENCFF000YRB.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/ctl1/ENCFF000YRB.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/ctl1/ENCFF000YRB.merged.nodup.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep1/pseudorep1/ENCFF000YMO.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep1/pseudorep2/ENCFF000YMO.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep1/ENCFF000YMO.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep1/ENCFF000YMO.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep1/ENCFF000YMO.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep2/pseudorep1/ENCFF000YMR.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep2/pseudorep2/ENCFF000YMR.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep2/ENCFF000YMR.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep2/ENCFF000YMR.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFU/align/rep2/ENCFF000YMR.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/peak/rep1/pseudorep1/ENCFF000YMO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep1/ENCFF000YMO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep1/ENCFF000YMO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep1/ENCFF000YMO.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep2/ENCFF000YMO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep2/ENCFF000YMO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep2/ENCFF000YMO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/pseudorep2/ENCFF000YMO.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/ENCFF000YMO.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/ENCFF000YMO.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/ENCFF000YMO.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep1/ENCFF000YMO.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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/peak/rep2/pseudorep1/ENCFF000YMR.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep1/ENCFF000YMR.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep1/ENCFF000YMR.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep1/ENCFF000YMR.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep2/ENCFF000YMR.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep2/ENCFF000YMR.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep2/ENCFF000YMR.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/pseudorep2/ENCFF000YMR.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/ENCFF000YMR.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/ENCFF000YMR.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/ENCFF000YMR.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFU/peak/rep2/ENCFF000YMR.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/ctl1/ENCFF000YRB.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/ctl1/ENCFF000YRB.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/ctl1/ENCFF000YRB.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/ctl1/ENCFF000YRB.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/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/ENCSR000EFU/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/qc/rep1/pseudorep1/ENCFF000YMO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/pseudorep2/ENCFF000YMO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep1/ENCFF000YMO.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/qc/rep2/pseudorep1/ENCFF000YMR.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/pseudorep2/ENCFF000YMR.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/rep2/ENCFF000YMR.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/ENCFF000YMO.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000EFU/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFU/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFU/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/ENCSR000EFU/signal/rep1/ENCFF000YMO.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFU/signal/rep1/ENCFF000YMO.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFU/signal/rep2/ENCFF000YMR.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFU/signal/rep2/ENCFF000YMR.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 4936378848054511275 chip.macs2_signal_track_pooled 1126756517014616842 BW p-val 4936378848054511275->1126756517014616842 6957848900548151641 BW FC 4936378848054511275->6957848900548151641 -4719468693541547600 chip.call_peak_pooled -8344812759806379754 Peak (bfilt) -4719468693541547600->-8344812759806379754 1859452853463400745 Peak -4719468693541547600->1859452853463400745 3030305349185861561 chip.idr_ppr 1859452853463400745->3030305349185861561 8667474216251699084 chip.idr 1859452853463400745->8667474216251699084 -8342014309913144096 chip.overlap 1859452853463400745->-8342014309913144096 -8226181906565218386 chip.overlap_ppr 1859452853463400745->-8226181906565218386 -7779497108470378041 chip.pool_ta 1544735054956913961 TAG-ALIGN -7779497108470378041->1544735054956913961 1544735054956913961->4936378848054511275 1544735054956913961->-4719468693541547600 -3277369667592844361 chip.call_peak 1544735054956913961->-3277369667592844361 -3020243932451715387 chip.macs2_signal_track 1544735054956913961->-3020243932451715387 6719393852944439652 chip.call_peak 1544735054956913961->6719393852944439652 4384289769758412503 chip.macs2_signal_track 1544735054956913961->4384289769758412503 1544735054956913961->3030305349185861561 1544735054956913961->8667474216251699084 1544735054956913961->-8342014309913144096 -347596077479614060 chip.reproducibility_overlap 1544735054956913961->-347596077479614060 -1159188386538633179 chip.reproducibility_idr 1544735054956913961->-1159188386538633179 1544735054956913961->-8226181906565218386 2071473480389908558 Peak (bfilt) -3277369667592844361->2071473480389908558 -4157276442699333758 Peak -3277369667592844361->-4157276442699333758 -4157276442699333758->8667474216251699084 -4157276442699333758->-8342014309913144096 -4157276442699333758->-347596077479614060 -4157276442699333758->-1159188386538633179 -3167484274342384629 chip.bam2ta 3695570349250225798 TAG-ALIGN -3167484274342384629->3695570349250225798 3695570349250225798->-7779497108470378041 3695570349250225798->-3277369667592844361 3695570349250225798->-3020243932451715387 3695570349250225798->6719393852944439652 3695570349250225798->4384289769758412503 3695570349250225798->3030305349185861561 3695570349250225798->-347596077479614060 3695570349250225798->-1159188386538633179 3695570349250225798->-8226181906565218386 4408308247044854082 chip.filter 554990039802529956 SAMstats QC 4408308247044854082->554990039802529956 -3882237708770563067 Filt/deduped BAM 4408308247044854082->-3882237708770563067 7561639486860908472 LibCmplx QC 4408308247044854082->7561639486860908472 -3882237708770563067->-3167484274342384629 822929061328072407 chip.jsd -3882237708770563067->822929061328072407 437087568254993454 chip.align 7214745853064114629 BAM 437087568254993454->7214745853064114629 -8050691959801395181 SAMstats QC 437087568254993454->-8050691959801395181 7214745853064114629->4408308247044854082 7540285707637763576 chip.xcor 4125399252145476230 XCOR Plot 7540285707637763576->4125399252145476230 6279534258370471383 BW p-val -3020243932451715387->6279534258370471383 3141798564204532301 BW FC -3020243932451715387->3141798564204532301 -2074078961487762364 FASTQ R1 (1) -2074078961487762364->437087568254993454 -2074078961487762364->7540285707637763576 -2895124374513476104 Peak (bfilt) 6719393852944439652->-2895124374513476104 -4665223068547026271 Peak 6719393852944439652->-4665223068547026271 -4665223068547026271->8667474216251699084 -4665223068547026271->-8342014309913144096 -4665223068547026271->-347596077479614060 -4665223068547026271->-1159188386538633179 -6861557096825732410 chip.bam2ta -4854568262625555149 TAG-ALIGN -6861557096825732410->-4854568262625555149 -4854568262625555149->-7779497108470378041 -4854568262625555149->-3277369667592844361 -4854568262625555149->-3020243932451715387 -4854568262625555149->6719393852944439652 -4854568262625555149->4384289769758412503 -4854568262625555149->3030305349185861561 -4854568262625555149->-347596077479614060 -4854568262625555149->-1159188386538633179 -4854568262625555149->-8226181906565218386 2417497409299608559 chip.filter -4627087792646853577 SAMstats QC 2417497409299608559->-4627087792646853577 8828775785198750804 Filt/deduped BAM 2417497409299608559->8828775785198750804 -7341017351773846023 LibCmplx QC 2417497409299608559->-7341017351773846023 8828775785198750804->-6861557096825732410 8828775785198750804->822929061328072407 -1370856386389393441 chip.align -2970086902436941258 SAMstats QC -1370856386389393441->-2970086902436941258 -2980946141197597355 BAM -1370856386389393441->-2980946141197597355 -2980946141197597355->2417497409299608559 3197075383967516360 chip.xcor -673808941145686763 XCOR Plot 3197075383967516360->-673808941145686763 7920782393314055242 BW FC 4384289769758412503->7920782393314055242 -552560379970740205 BW p-val 4384289769758412503->-552560379970740205 6074046836891871298 FASTQ R1 (1) 6074046836891871298->-1370856386389393441 6074046836891871298->3197075383967516360 3017730458630879497 chip.bam2ta_ctl -6328987027047290268 TAG-ALIGN 3017730458630879497->-6328987027047290268 -6328987027047290268->4936378848054511275 -6328987027047290268->-4719468693541547600 -6328987027047290268->-3277369667592844361 -6328987027047290268->-3020243932451715387 -6328987027047290268->6719393852944439652 -6328987027047290268->4384289769758412503 -6328987027047290268->3030305349185861561 -6328987027047290268->-347596077479614060 -6328987027047290268->-1159188386538633179 -6328987027047290268->-8226181906565218386 8436807008414958919 chip.filter_ctl -7463423013507750426 SAMstats QC 8436807008414958919->-7463423013507750426 -1794598306735188184 Filt/deduped BAM 8436807008414958919->-1794598306735188184 3657152000703793172 LibCmplx QC 8436807008414958919->3657152000703793172 -1794598306735188184->3017730458630879497 -1794598306735188184->822929061328072407 -8374270165132049444 chip.align_ctl 321610305771049667 SAMstats QC -8374270165132049444->321610305771049667 7493803810132133598 BAM -8374270165132049444->7493803810132133598 7493803810132133598->8436807008414958919 -4160653192447112356 FASTQ R1 (1) -4160653192447112356->-8374270165132049444 3651573416333171909 IDR Plot ppr 3030305349185861561->3651573416333171909 8655008906548246513 IDR Peak ppr 3030305349185861561->8655008906548246513 8655008906548246513->-1159188386538633179 3407925215977776271 IDR Plot rep1_vs_rep2 8667474216251699084->3407925215977776271 4828819311735555518 IDR NPeak rep1_vs_rep2 8667474216251699084->4828819311735555518 4828819311735555518->-1159188386538633179 -2521457037089886068 Overlap Peak rep1_vs_rep2 -8342014309913144096->-2521457037089886068 -2521457037089886068->-347596077479614060 -724918166897909235 Overlap Peak optimal -347596077479614060->-724918166897909235 8602651873396662953 Overlap reproducibility -347596077479614060->8602651873396662953 129202885470560285 IDR Peak optimal -1159188386538633179->129202885470560285 -2938763504555854684 IDR reproducibility -1159188386538633179->-2938763504555854684 -317382729879700157 Overlap Peak ppr -8226181906565218386->-317382729879700157 -317382729879700157->-347596077479614060 -5630281385761733017 JSD Plot 822929061328072407->-5630281385761733017

UCSC browser tracks

UCSC track hub plain text 
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