File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/ctl1/ENCFF000YRB.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/ctl1/ENCFF000YRB.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/ctl1/ENCFF000YRB.merged.nodup.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep1/pseudorep1/ENCFF000YZX.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep1/pseudorep2/ENCFF000YZX.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep1/ENCFF000YZX.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep1/ENCFF000YZX.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep1/ENCFF000YZX.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep2/pseudorep1/ENCFF000YZY.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep2/pseudorep2/ENCFF000YZY.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep2/ENCFF000YZY.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep2/ENCFF000YZY.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EGW/align/rep2/ENCFF000YZY.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/peak/rep1/pseudorep1/ENCFF000YZX.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep1/ENCFF000YZX.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep1/ENCFF000YZX.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep1/ENCFF000YZX.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep2/ENCFF000YZX.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep2/ENCFF000YZX.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep2/ENCFF000YZX.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/pseudorep2/ENCFF000YZX.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/ENCFF000YZX.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/ENCFF000YZX.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/ENCFF000YZX.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep1/ENCFF000YZX.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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/peak/rep2/pseudorep1/ENCFF000YZY.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep1/ENCFF000YZY.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep1/ENCFF000YZY.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep1/ENCFF000YZY.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep2/ENCFF000YZY.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep2/ENCFF000YZY.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep2/ENCFF000YZY.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/pseudorep2/ENCFF000YZY.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/ENCFF000YZY.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/ENCFF000YZY.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/ENCFF000YZY.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EGW/peak/rep2/ENCFF000YZY.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/ctl1/ENCFF000YRB.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/ctl1/ENCFF000YRB.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/ctl1/ENCFF000YRB.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/ctl1/ENCFF000YRB.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/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/ENCSR000EGW/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/qc/rep1/pseudorep1/ENCFF000YZX.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/pseudorep2/ENCFF000YZX.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep1/ENCFF000YZX.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/qc/rep2/pseudorep1/ENCFF000YZY.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/pseudorep2/ENCFF000YZY.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/rep2/ENCFF000YZY.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/ENCFF000YZX.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000EGW/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EGW/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EGW/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/ENCSR000EGW/signal/rep1/ENCFF000YZX.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EGW/signal/rep1/ENCFF000YZX.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EGW/signal/rep2/ENCFF000YZY.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EGW/signal/rep2/ENCFF000YZY.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 -1505224081915200042 chip.macs2_signal_track_pooled -7797577917614042807 BW p-val -1505224081915200042->-7797577917614042807 5659469415860390332 BW FC -1505224081915200042->5659469415860390332 -1030085695867095570 chip.call_peak_pooled -6217106512476634254 Peak (bfilt) -1030085695867095570->-6217106512476634254 -7257079038819964661 Peak -1030085695867095570->-7257079038819964661 -3233014308645262027 chip.idr_ppr -7257079038819964661->-3233014308645262027 -5669455069351292491 chip.idr -7257079038819964661->-5669455069351292491 -139466166988528053 chip.overlap -7257079038819964661->-139466166988528053 5806347089367486877 chip.overlap_ppr -7257079038819964661->5806347089367486877 5431462744509601606 chip.pool_ta -4296637198894533445 TAG-ALIGN 5431462744509601606->-4296637198894533445 -4296637198894533445->-1505224081915200042 -4296637198894533445->-1030085695867095570 -2936129327938210971 chip.call_peak -4296637198894533445->-2936129327938210971 -5948577903047304602 chip.macs2_signal_track -4296637198894533445->-5948577903047304602 -3555699831058802220 chip.call_peak -4296637198894533445->-3555699831058802220 6821847256415219623 chip.macs2_signal_track -4296637198894533445->6821847256415219623 -4296637198894533445->-3233014308645262027 -4296637198894533445->-5669455069351292491 -4296637198894533445->-139466166988528053 738120511114538424 chip.reproducibility_overlap -4296637198894533445->738120511114538424 -2270513940250802884 chip.reproducibility_idr -4296637198894533445->-2270513940250802884 -4296637198894533445->5806347089367486877 -6403693131663717233 Peak (bfilt) -2936129327938210971->-6403693131663717233 -2438221316078176727 Peak -2936129327938210971->-2438221316078176727 -2438221316078176727->-5669455069351292491 -2438221316078176727->-139466166988528053 -2438221316078176727->738120511114538424 -2438221316078176727->-2270513940250802884 3074050216864843087 chip.bam2ta 294162549852880974 TAG-ALIGN 3074050216864843087->294162549852880974 294162549852880974->5431462744509601606 294162549852880974->-2936129327938210971 294162549852880974->-5948577903047304602 294162549852880974->-3555699831058802220 294162549852880974->6821847256415219623 294162549852880974->-3233014308645262027 294162549852880974->738120511114538424 294162549852880974->-2270513940250802884 294162549852880974->5806347089367486877 -6383287143755907105 chip.filter 3987157098170648076 SAMstats QC -6383287143755907105->3987157098170648076 6378322215745494817 Filt/deduped BAM -6383287143755907105->6378322215745494817 -9016171856566349275 LibCmplx QC -6383287143755907105->-9016171856566349275 6378322215745494817->3074050216864843087 7875970391053138022 chip.jsd 6378322215745494817->7875970391053138022 -8527538520900201321 chip.align 6861030731880492291 SAMstats QC -8527538520900201321->6861030731880492291 -2002723798222954913 BAM -8527538520900201321->-2002723798222954913 -2002723798222954913->-6383287143755907105 2237331370556479713 chip.xcor 7080736020551367605 XCOR Plot 2237331370556479713->7080736020551367605 -3823425787886409874 BW p-val -5948577903047304602->-3823425787886409874 4766312427889335633 BW FC -5948577903047304602->4766312427889335633 2712819262046902584 FASTQ R1 (1) 2712819262046902584->-8527538520900201321 2712819262046902584->2237331370556479713 -7924258510626371767 Peak (bfilt) -3555699831058802220->-7924258510626371767 8476349351797348306 Peak -3555699831058802220->8476349351797348306 8476349351797348306->-5669455069351292491 8476349351797348306->-139466166988528053 8476349351797348306->738120511114538424 8476349351797348306->-2270513940250802884 -507160416910495790 chip.bam2ta -4241337042683229927 TAG-ALIGN -507160416910495790->-4241337042683229927 -4241337042683229927->5431462744509601606 -4241337042683229927->-2936129327938210971 -4241337042683229927->-5948577903047304602 -4241337042683229927->-3555699831058802220 -4241337042683229927->6821847256415219623 -4241337042683229927->-3233014308645262027 -4241337042683229927->738120511114538424 -4241337042683229927->-2270513940250802884 -4241337042683229927->5806347089367486877 4045894249242664278 chip.filter -150695541633147619 SAMstats QC 4045894249242664278->-150695541633147619 -8687107253837755634 Filt/deduped BAM 4045894249242664278->-8687107253837755634 -457708954865259492 LibCmplx QC 4045894249242664278->-457708954865259492 -8687107253837755634->-507160416910495790 -8687107253837755634->7875970391053138022 7158961031414924149 chip.align 8370698705070664398 BAM 7158961031414924149->8370698705070664398 -8588028729661125674 SAMstats QC 7158961031414924149->-8588028729661125674 8370698705070664398->4045894249242664278 -240781140684413564 chip.xcor 8440975900479710756 XCOR Plot -240781140684413564->8440975900479710756 4473931442332413601 BW FC 6821847256415219623->4473931442332413601 -8232834900015172514 BW p-val 6821847256415219623->-8232834900015172514 9014665330695063599 FASTQ R1 (1) 9014665330695063599->7158961031414924149 9014665330695063599->-240781140684413564 -1535029544492006945 chip.bam2ta_ctl -6427649819707726530 TAG-ALIGN -1535029544492006945->-6427649819707726530 -6427649819707726530->-1505224081915200042 -6427649819707726530->-1030085695867095570 -6427649819707726530->-2936129327938210971 -6427649819707726530->-5948577903047304602 -6427649819707726530->-3555699831058802220 -6427649819707726530->6821847256415219623 -6427649819707726530->-3233014308645262027 -6427649819707726530->738120511114538424 -6427649819707726530->-2270513940250802884 -6427649819707726530->5806347089367486877 -4116237426251142294 chip.filter_ctl 7510022958969941317 SAMstats QC -4116237426251142294->7510022958969941317 4615564997914586607 Filt/deduped BAM -4116237426251142294->4615564997914586607 -5949947083967956498 LibCmplx QC -4116237426251142294->-5949947083967956498 4615564997914586607->-1535029544492006945 4615564997914586607->7875970391053138022 4747035182476782543 chip.align_ctl -4319915304154459514 BAM 4747035182476782543->-4319915304154459514 -5430701486521494575 SAMstats QC 4747035182476782543->-5430701486521494575 -4319915304154459514->-4116237426251142294 -5654722820366802734 FASTQ R1 (1) -5654722820366802734->4747035182476782543 -5237264594660043497 IDR Plot ppr -3233014308645262027->-5237264594660043497 -3542630674965611836 IDR Peak ppr -3233014308645262027->-3542630674965611836 -3542630674965611836->-2270513940250802884 8184073511463109429 IDR Plot rep1_vs_rep2 -5669455069351292491->8184073511463109429 -5354170487078139395 IDR NPeak rep1_vs_rep2 -5669455069351292491->-5354170487078139395 -5354170487078139395->-2270513940250802884 1640125786535100988 Overlap Peak rep1_vs_rep2 -139466166988528053->1640125786535100988 1640125786535100988->738120511114538424 8154539380150155548 Overlap Peak optimal 738120511114538424->8154539380150155548 8187024142853304163 Overlap reproducibility 738120511114538424->8187024142853304163 2363568941272540057 IDR Peak optimal -2270513940250802884->2363568941272540057 4959398523231081416 IDR reproducibility -2270513940250802884->4959398523231081416 3480020264487361483 Overlap Peak ppr 5806347089367486877->3480020264487361483 3480020264487361483->738120511114538424 5853621535091779741 JSD Plot 7875970391053138022->5853621535091779741

UCSC browser tracks

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