File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/ctl1/ENCFF000YRB.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/ctl1/ENCFF000YRB.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/ctl1/ENCFF000YRB.merged.nodup.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep1/pseudorep1/ENCFF000YJJ.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep1/pseudorep2/ENCFF000YJJ.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep1/ENCFF000YJJ.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep1/ENCFF000YJJ.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep1/ENCFF000YJJ.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep2/pseudorep1/ENCFF000YJL.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep2/pseudorep2/ENCFF000YJL.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep2/ENCFF000YJL.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep2/ENCFF000YJL.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EFS/align/rep2/ENCFF000YJL.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/peak/rep1/pseudorep1/ENCFF000YJJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep1/ENCFF000YJJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep1/ENCFF000YJJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep1/ENCFF000YJJ.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep2/ENCFF000YJJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep2/ENCFF000YJJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep2/ENCFF000YJJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/pseudorep2/ENCFF000YJJ.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/ENCFF000YJJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/ENCFF000YJJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/ENCFF000YJJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep1/ENCFF000YJJ.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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/peak/rep2/pseudorep1/ENCFF000YJL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep1/ENCFF000YJL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep1/ENCFF000YJL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep1/ENCFF000YJL.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep2/ENCFF000YJL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep2/ENCFF000YJL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep2/ENCFF000YJL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/pseudorep2/ENCFF000YJL.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/ENCFF000YJL.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/ENCFF000YJL.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/ENCFF000YJL.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EFS/peak/rep2/ENCFF000YJL.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/ctl1/ENCFF000YRB.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/ctl1/ENCFF000YRB.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/ctl1/ENCFF000YRB.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/ctl1/ENCFF000YRB.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/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/ENCSR000EFS/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/qc/rep1/pseudorep1/ENCFF000YJJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/pseudorep2/ENCFF000YJJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep1/ENCFF000YJJ.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/qc/rep2/pseudorep1/ENCFF000YJL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/pseudorep2/ENCFF000YJL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/rep2/ENCFF000YJL.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/ENCFF000YJJ.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000EFS/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFS/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000YRB.merged.nodup.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFS/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/ENCSR000EFS/signal/rep1/ENCFF000YJJ.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFS/signal/rep1/ENCFF000YJJ.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EFS/signal/rep2/ENCFF000YJL.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EFS/signal/rep2/ENCFF000YJL.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 -8809325618004975559 chip.macs2_signal_track_pooled -506382050170744372 BW FC -8809325618004975559->-506382050170744372 1420697063458112464 BW p-val -8809325618004975559->1420697063458112464 8720858933832549183 chip.call_peak_pooled -2117666192158135534 Peak (bfilt) 8720858933832549183->-2117666192158135534 -7102119646204980827 Peak 8720858933832549183->-7102119646204980827 5000159583436448634 chip.idr_ppr -7102119646204980827->5000159583436448634 -3291106438440525959 chip.idr -7102119646204980827->-3291106438440525959 -2244680870322917454 chip.overlap -7102119646204980827->-2244680870322917454 661241557929494714 chip.overlap_ppr -7102119646204980827->661241557929494714 2796330228591359868 chip.pool_ta 8705338600297960932 TAG-ALIGN 2796330228591359868->8705338600297960932 8705338600297960932->-8809325618004975559 8705338600297960932->8720858933832549183 1691433006239070633 chip.call_peak 8705338600297960932->1691433006239070633 -8290523458231023996 chip.macs2_signal_track 8705338600297960932->-8290523458231023996 4865723810059300448 chip.call_peak 8705338600297960932->4865723810059300448 -1515769144934026575 chip.macs2_signal_track 8705338600297960932->-1515769144934026575 8705338600297960932->5000159583436448634 8705338600297960932->-3291106438440525959 8705338600297960932->-2244680870322917454 4262383507679074128 chip.reproducibility_overlap 8705338600297960932->4262383507679074128 69302794756102179 chip.reproducibility_idr 8705338600297960932->69302794756102179 8705338600297960932->661241557929494714 -7799312474920585690 Peak (bfilt) 1691433006239070633->-7799312474920585690 -8447090892047274336 Peak 1691433006239070633->-8447090892047274336 -8447090892047274336->-3291106438440525959 -8447090892047274336->-2244680870322917454 -8447090892047274336->4262383507679074128 -8447090892047274336->69302794756102179 -7827697688390063808 chip.bam2ta 7579189517344661583 TAG-ALIGN -7827697688390063808->7579189517344661583 7579189517344661583->2796330228591359868 7579189517344661583->1691433006239070633 7579189517344661583->-8290523458231023996 7579189517344661583->4865723810059300448 7579189517344661583->-1515769144934026575 7579189517344661583->5000159583436448634 7579189517344661583->4262383507679074128 7579189517344661583->69302794756102179 7579189517344661583->661241557929494714 -2861264694217150274 chip.filter 6470969196303413785 SAMstats QC -2861264694217150274->6470969196303413785 97639471700184993 Filt/deduped BAM -2861264694217150274->97639471700184993 5740071172419243169 LibCmplx QC -2861264694217150274->5740071172419243169 97639471700184993->-7827697688390063808 -1444439052411612495 chip.jsd 97639471700184993->-1444439052411612495 7958884974170517960 chip.align -4581951201911739943 BAM 7958884974170517960->-4581951201911739943 4894702299563832885 SAMstats QC 7958884974170517960->4894702299563832885 -4581951201911739943->-2861264694217150274 -1841361093505196572 chip.xcor -7066049670081245939 XCOR Plot -1841361093505196572->-7066049670081245939 1652577402927464901 BW p-val -8290523458231023996->1652577402927464901 2911404050202480265 BW FC -8290523458231023996->2911404050202480265 -2275950762908611672 FASTQ R1 (1) -2275950762908611672->7958884974170517960 -2275950762908611672->-1841361093505196572 2838254491445294027 Peak (bfilt) 4865723810059300448->2838254491445294027 8481488166109464402 Peak 4865723810059300448->8481488166109464402 8481488166109464402->-3291106438440525959 8481488166109464402->-2244680870322917454 8481488166109464402->4262383507679074128 8481488166109464402->69302794756102179 -4609836812094307439 chip.bam2ta -5214537129538825556 TAG-ALIGN -4609836812094307439->-5214537129538825556 -5214537129538825556->2796330228591359868 -5214537129538825556->1691433006239070633 -5214537129538825556->-8290523458231023996 -5214537129538825556->4865723810059300448 -5214537129538825556->-1515769144934026575 -5214537129538825556->5000159583436448634 -5214537129538825556->4262383507679074128 -5214537129538825556->69302794756102179 -5214537129538825556->661241557929494714 -7399459118934312625 chip.filter -4053447713565306783 SAMstats QC -7399459118934312625->-4053447713565306783 2960222485144802062 Filt/deduped BAM -7399459118934312625->2960222485144802062 9125237859037210500 LibCmplx QC -7399459118934312625->9125237859037210500 2960222485144802062->-4609836812094307439 2960222485144802062->-1444439052411612495 3364244044869733505 chip.align 7692792973041028116 BAM 3364244044869733505->7692792973041028116 6922345709346621110 SAMstats QC 3364244044869733505->6922345709346621110 7692792973041028116->-7399459118934312625 6696043154873318851 chip.xcor -4328102643919827034 XCOR Plot 6696043154873318851->-4328102643919827034 3805294490179987166 BW FC -1515769144934026575->3805294490179987166 1588735259111563172 BW p-val -1515769144934026575->1588735259111563172 1976687729565350096 FASTQ R1 (1) 1976687729565350096->3364244044869733505 1976687729565350096->6696043154873318851 -1451911086563329909 chip.bam2ta_ctl 4572053291412944890 TAG-ALIGN -1451911086563329909->4572053291412944890 4572053291412944890->-8809325618004975559 4572053291412944890->8720858933832549183 4572053291412944890->1691433006239070633 4572053291412944890->-8290523458231023996 4572053291412944890->4865723810059300448 4572053291412944890->-1515769144934026575 4572053291412944890->5000159583436448634 4572053291412944890->4262383507679074128 4572053291412944890->69302794756102179 4572053291412944890->661241557929494714 7235403692619593905 chip.filter_ctl -7872098764713508098 SAMstats QC 7235403692619593905->-7872098764713508098 2004430985377954095 Filt/deduped BAM 7235403692619593905->2004430985377954095 8115165099855380958 LibCmplx QC 7235403692619593905->8115165099855380958 2004430985377954095->-1451911086563329909 2004430985377954095->-1444439052411612495 -3819001864932438267 chip.align_ctl 6298012723089879181 SAMstats QC -3819001864932438267->6298012723089879181 4938069745767469276 BAM -3819001864932438267->4938069745767469276 4938069745767469276->7235403692619593905 9088633831515246231 FASTQ R1 (1) 9088633831515246231->-3819001864932438267 8812335216833776358 IDR Plot ppr 5000159583436448634->8812335216833776358 -8036873019956480831 IDR Peak ppr 5000159583436448634->-8036873019956480831 -8036873019956480831->69302794756102179 6671302881894993032 IDR Plot rep1_vs_rep2 -3291106438440525959->6671302881894993032 -1819844530438134779 IDR NPeak rep1_vs_rep2 -3291106438440525959->-1819844530438134779 -1819844530438134779->69302794756102179 7988679817397477090 Overlap Peak rep1_vs_rep2 -2244680870322917454->7988679817397477090 7988679817397477090->4262383507679074128 -4970006930251626476 Overlap Peak optimal 4262383507679074128->-4970006930251626476 7138445051910545521 Overlap reproducibility 4262383507679074128->7138445051910545521 -3208723192031004800 IDR Peak optimal 69302794756102179->-3208723192031004800 -8650426731392646931 IDR reproducibility 69302794756102179->-8650426731392646931 -8430330255738456420 Overlap Peak ppr 661241557929494714->-8430330255738456420 -8430330255738456420->4262383507679074128 -5048878048518834856 JSD Plot -1444439052411612495->-5048878048518834856

UCSC browser tracks

UCSC track hub plain text 
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UCSC track hub encoded URL (Use this for browser's parameter &hgct_customText=) 
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