File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/ctl1/ENCFF000VWV.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/ctl1/ENCFF000VWV.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/ctl1/ENCFF000VWV.merged.nodup.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep1/pseudorep1/ENCFF000VVP.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep1/pseudorep2/ENCFF000VVP.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep1/ENCFF000VVP.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep1/ENCFF000VVP.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep1/ENCFF000VVP.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep2/pseudorep1/ENCFF000VVQ.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep2/pseudorep2/ENCFF000VVQ.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep2/ENCFF000VVQ.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep2/ENCFF000VVQ.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DZQ/align/rep2/ENCFF000VVQ.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/peak/rep1/pseudorep1/ENCFF000VVP.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep1/ENCFF000VVP.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep1/ENCFF000VVP.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep1/ENCFF000VVP.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep2/ENCFF000VVP.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep2/ENCFF000VVP.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep2/ENCFF000VVP.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/pseudorep2/ENCFF000VVP.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/ENCFF000VVP.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/ENCFF000VVP.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/ENCFF000VVP.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep1/ENCFF000VVP.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/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/peak/rep2/pseudorep1/ENCFF000VVQ.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep1/ENCFF000VVQ.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep1/ENCFF000VVQ.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep1/ENCFF000VVQ.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep2/ENCFF000VVQ.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep2/ENCFF000VVQ.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep2/ENCFF000VVQ.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/pseudorep2/ENCFF000VVQ.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/ENCFF000VVQ.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/ENCFF000VVQ.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/ENCFF000VVQ.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DZQ/peak/rep2/ENCFF000VVQ.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/ctl1/ENCFF000VWV.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/ctl1/ENCFF000VWV.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/ctl1/ENCFF000VWV.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/ctl1/ENCFF000VWV.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/qc/pooled-rep/pseudorep1/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/pooled-rep/pseudorep2/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.frip.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/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/ENCSR000DZQ/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/qc/rep1/pseudorep1/ENCFF000VVP.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/pseudorep2/ENCFF000VVP.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep1/ENCFF000VVP.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/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/ENCSR000DZQ/qc/rep2/pseudorep1/ENCFF000VVQ.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/pseudorep2/ENCFF000VVQ.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/rep2/ENCFF000VVQ.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/ENCFF000VVP.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000DZQ/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/signal/pooled-rep/basename_prefix.pooled_x_ENCFF000VWV.merged.nodup.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/signal/rep1/ENCFF000VVP.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/signal/rep1/ENCFF000VVP.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/signal/rep2/ENCFF000VVQ.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000DZQ/signal/rep2/ENCFF000VVQ.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 -7811893270764127578 chip.macs2_signal_track_pooled 1460832893681644592 BW FC -7811893270764127578->1460832893681644592 4436453075133114206 BW p-val -7811893270764127578->4436453075133114206 -5457552648048277514 chip.call_peak_pooled 6225275629026031650 Peak (bfilt) -5457552648048277514->6225275629026031650 -1919766050957451182 Peak -5457552648048277514->-1919766050957451182 -8479263130159482168 chip.idr_ppr -1919766050957451182->-8479263130159482168 2384358099338792285 chip.idr -1919766050957451182->2384358099338792285 -3275994863033050413 chip.overlap -1919766050957451182->-3275994863033050413 3270789738828385461 chip.overlap_ppr -1919766050957451182->3270789738828385461 6393821996202940889 chip.pool_ta -2590935529450190636 TAG-ALIGN 6393821996202940889->-2590935529450190636 -2590935529450190636->-7811893270764127578 -2590935529450190636->-5457552648048277514 4770639281452504789 chip.call_peak -2590935529450190636->4770639281452504789 5695507095260068258 chip.macs2_signal_track -2590935529450190636->5695507095260068258 638843354036488734 chip.call_peak -2590935529450190636->638843354036488734 7457985789660788169 chip.macs2_signal_track -2590935529450190636->7457985789660788169 -2590935529450190636->-8479263130159482168 -2590935529450190636->2384358099338792285 -2590935529450190636->-3275994863033050413 2170355682264777803 chip.reproducibility_overlap -2590935529450190636->2170355682264777803 -842942370250537785 chip.reproducibility_idr -2590935529450190636->-842942370250537785 -2590935529450190636->3270789738828385461 4373541504315719491 Peak (bfilt) 4770639281452504789->4373541504315719491 -7471846809416998823 Peak 4770639281452504789->-7471846809416998823 -7471846809416998823->2384358099338792285 -7471846809416998823->-3275994863033050413 -7471846809416998823->2170355682264777803 -7471846809416998823->-842942370250537785 -5655207719117094118 chip.bam2ta -7275347333930657821 TAG-ALIGN -5655207719117094118->-7275347333930657821 -7275347333930657821->6393821996202940889 -7275347333930657821->4770639281452504789 -7275347333930657821->5695507095260068258 -7275347333930657821->638843354036488734 -7275347333930657821->7457985789660788169 -7275347333930657821->-8479263130159482168 -7275347333930657821->2170355682264777803 -7275347333930657821->-842942370250537785 -7275347333930657821->3270789738828385461 2258849665637750302 chip.filter -6337287051053557850 SAMstats QC 2258849665637750302->-6337287051053557850 334619947636589797 Filt/deduped BAM 2258849665637750302->334619947636589797 1709086326211111928 LibCmplx QC 2258849665637750302->1709086326211111928 334619947636589797->-5655207719117094118 4014458390885711843 chip.jsd 334619947636589797->4014458390885711843 2273581251226893457 chip.align 7885796181857807569 SAMstats QC 2273581251226893457->7885796181857807569 4414854911432626094 BAM 2273581251226893457->4414854911432626094 4414854911432626094->2258849665637750302 -4411498157246454259 chip.xcor -1681759904997008018 XCOR Plot -4411498157246454259->-1681759904997008018 -429945153887255737 BW FC 5695507095260068258->-429945153887255737 6554872884311054801 BW p-val 5695507095260068258->6554872884311054801 -4706573491891381484 FASTQ R1 (1) -4706573491891381484->2273581251226893457 -4706573491891381484->-4411498157246454259 4947867684967263169 Peak (bfilt) 638843354036488734->4947867684967263169 -3157264899732658890 Peak 638843354036488734->-3157264899732658890 -3157264899732658890->2384358099338792285 -3157264899732658890->-3275994863033050413 -3157264899732658890->2170355682264777803 -3157264899732658890->-842942370250537785 -9174832970155221474 chip.bam2ta 7504709220381487944 TAG-ALIGN -9174832970155221474->7504709220381487944 7504709220381487944->6393821996202940889 7504709220381487944->4770639281452504789 7504709220381487944->5695507095260068258 7504709220381487944->638843354036488734 7504709220381487944->7457985789660788169 7504709220381487944->-8479263130159482168 7504709220381487944->2170355682264777803 7504709220381487944->-842942370250537785 7504709220381487944->3270789738828385461 6034468804748772415 chip.filter 2911866162546887749 SAMstats QC 6034468804748772415->2911866162546887749 -2338851894916194361 Filt/deduped BAM 6034468804748772415->-2338851894916194361 -4604373091214564207 LibCmplx QC 6034468804748772415->-4604373091214564207 -2338851894916194361->-9174832970155221474 -2338851894916194361->4014458390885711843 5363914308626837015 chip.align -6010177761219065823 SAMstats QC 5363914308626837015->-6010177761219065823 4633813386239550658 BAM 5363914308626837015->4633813386239550658 4633813386239550658->6034468804748772415 2417646299388113009 chip.xcor -4484937369337262039 XCOR Plot 2417646299388113009->-4484937369337262039 4136120475006741542 BW FC 7457985789660788169->4136120475006741542 -2076048819099830506 BW p-val 7457985789660788169->-2076048819099830506 -6495010560525509399 FASTQ R1 (1) -6495010560525509399->5363914308626837015 -6495010560525509399->2417646299388113009 2471935823943655275 chip.bam2ta_ctl -8800285631050735803 TAG-ALIGN 2471935823943655275->-8800285631050735803 -8800285631050735803->-7811893270764127578 -8800285631050735803->-5457552648048277514 -8800285631050735803->4770639281452504789 -8800285631050735803->5695507095260068258 -8800285631050735803->638843354036488734 -8800285631050735803->7457985789660788169 -8800285631050735803->-8479263130159482168 -8800285631050735803->2170355682264777803 -8800285631050735803->-842942370250537785 -8800285631050735803->3270789738828385461 -9198280600388923298 chip.filter_ctl -6864074355482841539 SAMstats QC -9198280600388923298->-6864074355482841539 8121928904561720899 Filt/deduped BAM -9198280600388923298->8121928904561720899 7347753093762945547 LibCmplx QC -9198280600388923298->7347753093762945547 8121928904561720899->2471935823943655275 8121928904561720899->4014458390885711843 -2630027062120431251 chip.align_ctl 8287136723281103707 SAMstats QC -2630027062120431251->8287136723281103707 -8988778036865656124 BAM -2630027062120431251->-8988778036865656124 -8988778036865656124->-9198280600388923298 -4795678428297656169 FASTQ R1 (1) -4795678428297656169->-2630027062120431251 3521476244499196247 IDR Plot ppr -8479263130159482168->3521476244499196247 2940350749816784638 IDR Peak ppr -8479263130159482168->2940350749816784638 2940350749816784638->-842942370250537785 5399451730499777228 IDR Plot rep1_vs_rep2 2384358099338792285->5399451730499777228 -7849867201332736377 IDR NPeak rep1_vs_rep2 2384358099338792285->-7849867201332736377 -7849867201332736377->-842942370250537785 -4262246683228833626 Overlap Peak rep1_vs_rep2 -3275994863033050413->-4262246683228833626 -4262246683228833626->2170355682264777803 -7537497554147524515 Overlap Peak optimal 2170355682264777803->-7537497554147524515 9177685384216520537 Overlap reproducibility 2170355682264777803->9177685384216520537 1218894279585046139 IDR Peak optimal -842942370250537785->1218894279585046139 -2552679106770321114 IDR reproducibility -842942370250537785->-2552679106770321114 2605800938177229028 Overlap Peak ppr 3270789738828385461->2605800938177229028 2605800938177229028->2170355682264777803 -3108648640822855655 JSD Plot 4014458390885711843->-3108648640822855655

UCSC browser tracks

UCSC track hub plain text 
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