File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/se/align/ctl1/ctl1.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/se/align/ctl1/ctl1.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/ctl1/ctl1.merged.nodup.tagAlign.gz
Control 2
Filtered BAM/srv/www/kundaje/natprot_chip/se/align/ctl2/ctl2.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/se/align/ctl2/ctl2.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/ctl2/ctl2.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/pooled-ctl/ctl1.merged.nodup.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/pooled-rep/pseudorep1/rep1.merged.nodup.pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/pooled-rep/pseudorep2/rep1.merged.nodup.pr2.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/pooled-rep/rep1.merged.nodup.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/rep1/pseudorep1/rep1.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/rep1/pseudorep2/rep1.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/se/align/rep1/rep1.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/se/align/rep1/rep1.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/rep1/rep1.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/rep2/pseudorep1/rep2.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/rep2/pseudorep2/rep2.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/se/align/rep2/rep2.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/se/align/rep2/rep2.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/se/align/rep2/rep2.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/se/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/se/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/se/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/se/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/se/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/se/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/se/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/se/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/se/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/se/peak/pooled-rep/pseudorep1/rep1.merged.nodup.pr1.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep1/rep1.merged.nodup.pr1.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep1/rep1.merged.nodup.pr1.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep1/rep1.merged.nodup.pr1.pooled_x_ctl1.merged.nodup.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep2/rep1.merged.nodup.pr2.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep2/rep1.merged.nodup.pr2.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep2/rep1.merged.nodup.pr2.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/pseudorep2/rep1.merged.nodup.pr2.pooled_x_ctl1.merged.nodup.pooled.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/se/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/se/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/se/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/se/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/se/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/se/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/se/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/se/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/se/peak/rep1/pseudorep1/rep1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep1/rep1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep1/rep1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep1/rep1.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep2/rep1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep2/rep1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep2/rep1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep1/pseudorep2/rep1.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep1/rep1.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep1/rep1.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep1/rep1.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep1/rep1.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/se/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/se/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/se/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/se/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/se/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/se/peak/rep2/pseudorep1/rep2.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep1/rep2.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep1/rep2.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep1/rep2.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep2/rep2.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep2/rep2.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep2/rep2.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep2/pseudorep2/rep2.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep2/rep2.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/se/peak/rep2/rep2.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/se/peak/rep2/rep2.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/se/peak/rep2/rep2.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/ctl1/ctl1.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/ctl1/ctl1.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/se/qc/ctl1/ctl1.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/ctl1/ctl1.merged.nodup.samstats.qc
Control 2
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/ctl2/ctl2.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/ctl2/ctl2.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/se/qc/ctl2/ctl2.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/ctl2/ctl2.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/se/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/se/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/se/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/se/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/se/qc/pooled-rep/pseudorep1/rep1.merged.nodup.pr1.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/se/qc/pooled-rep/pseudorep2/rep1.merged.nodup.pr2.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.frip.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/se/qc/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/se/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/se/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/se/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/se/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/se/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/se/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/se/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/se/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/se/qc/rep1/pseudorep1/rep1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/se/qc/rep1/pseudorep2/rep1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/rep1/rep1.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/se/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/se/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/se/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/se/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/se/qc/rep2/pseudorep1/rep2.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/se/qc/rep2/pseudorep2/rep2.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/se/qc/rep2/rep2.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/se/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/se/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/se/qc/rep1.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/se/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/se/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/se/signal/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/se/signal/pooled-rep/rep1.merged.nodup.pooled_x_ctl1.merged.nodup.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/se/signal/rep1/rep1.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/se/signal/rep1/rep1.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/se/signal/rep2/rep2.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/se/signal/rep2/rep2.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_pooled_ctl Pooled control cluster_ctl1 Control 1 cluster_ctl2 Control 2 7826884721671710988 chip.macs2_signal_track_pooled 1015922598178198520 BW FC 7826884721671710988->1015922598178198520 1228883238354702217 BW p-val 7826884721671710988->1228883238354702217 -4392080887455103667 chip.call_peak_pooled 7280702655607918587 Peak (bfilt) -4392080887455103667->7280702655607918587 -2525710795302346916 Peak -4392080887455103667->-2525710795302346916 6112888275474714771 chip.idr_ppr -2525710795302346916->6112888275474714771 5427617540906612683 chip.idr -2525710795302346916->5427617540906612683 2246475207573981792 chip.overlap -2525710795302346916->2246475207573981792 -4714068378521426992 chip.overlap_ppr -2525710795302346916->-4714068378521426992 -1126928004707876420 chip.pool_ta 6120255231820501058 TAG-ALIGN -1126928004707876420->6120255231820501058 6120255231820501058->7826884721671710988 6120255231820501058->-4392080887455103667 -8121313071353540249 chip.call_peak 6120255231820501058->-8121313071353540249 302008383341661453 chip.macs2_signal_track 6120255231820501058->302008383341661453 6500479434923217917 chip.call_peak 6120255231820501058->6500479434923217917 1529647233907073739 chip.macs2_signal_track 6120255231820501058->1529647233907073739 6120255231820501058->6112888275474714771 6120255231820501058->5427617540906612683 6120255231820501058->2246475207573981792 -4931438000231078795 chip.reproducibility_overlap 6120255231820501058->-4931438000231078795 -3582356986900019706 chip.reproducibility_idr 6120255231820501058->-3582356986900019706 6120255231820501058->-4714068378521426992 -1353232597030600399 Peak (bfilt) -8121313071353540249->-1353232597030600399 1320469397042977627 Peak -8121313071353540249->1320469397042977627 1320469397042977627->5427617540906612683 1320469397042977627->2246475207573981792 1320469397042977627->-4931438000231078795 1320469397042977627->-3582356986900019706 2425122069258831345 chip.bam2ta -11104391512770710 TAG-ALIGN 2425122069258831345->-11104391512770710 -11104391512770710->-1126928004707876420 -11104391512770710->-8121313071353540249 -11104391512770710->302008383341661453 -11104391512770710->6500479434923217917 -11104391512770710->1529647233907073739 -11104391512770710->6112888275474714771 -11104391512770710->-4931438000231078795 -11104391512770710->-3582356986900019706 -11104391512770710->-4714068378521426992 1182738717240186289 chip.filter -5547990748864420734 SAMstats QC 1182738717240186289->-5547990748864420734 -1850470985036115038 Filt/deduped BAM 1182738717240186289->-1850470985036115038 2339045648309598266 LibCmplx QC 1182738717240186289->2339045648309598266 -1850470985036115038->2425122069258831345 -8893690107086681214 chip.jsd -1850470985036115038->-8893690107086681214 -1975888110303411459 chip.align 3209201670931687446 BAM -1975888110303411459->3209201670931687446 -4291856536771742842 SAMstats QC -1975888110303411459->-4291856536771742842 3209201670931687446->1182738717240186289 3775241399556645594 chip.xcor -2318120306107118097 XCOR Plot 3775241399556645594->-2318120306107118097 1362027008417329998 BW p-val 302008383341661453->1362027008417329998 -4880046683002806889 BW FC 302008383341661453->-4880046683002806889 -2831318768417138570 FASTQ R1 (1) -2831318768417138570->-1975888110303411459 -2831318768417138570->3775241399556645594 -9199588218254408340 Peak (bfilt) 6500479434923217917->-9199588218254408340 1925693681820324691 Peak 6500479434923217917->1925693681820324691 1925693681820324691->5427617540906612683 1925693681820324691->2246475207573981792 1925693681820324691->-4931438000231078795 1925693681820324691->-3582356986900019706 -8617013070056838487 chip.bam2ta 532188351776508479 TAG-ALIGN -8617013070056838487->532188351776508479 532188351776508479->-1126928004707876420 532188351776508479->-8121313071353540249 532188351776508479->302008383341661453 532188351776508479->6500479434923217917 532188351776508479->1529647233907073739 532188351776508479->6112888275474714771 532188351776508479->-4931438000231078795 532188351776508479->-3582356986900019706 532188351776508479->-4714068378521426992 2619706586176298391 chip.filter 5244594449242309514 SAMstats QC 2619706586176298391->5244594449242309514 2775774201040508226 Filt/deduped BAM 2619706586176298391->2775774201040508226 -1085823682207251363 LibCmplx QC 2619706586176298391->-1085823682207251363 2775774201040508226->-8617013070056838487 2775774201040508226->-8893690107086681214 -8076412911421071267 chip.align 1853557983408791993 SAMstats QC -8076412911421071267->1853557983408791993 -6197635924274130041 BAM -8076412911421071267->-6197635924274130041 -6197635924274130041->2619706586176298391 -3799845014019419063 chip.xcor -7314004788457243908 XCOR Plot -3799845014019419063->-7314004788457243908 -6675766420415546062 BW FC 1529647233907073739->-6675766420415546062 -6158179573000255972 BW p-val 1529647233907073739->-6158179573000255972 -9145914672239476017 FASTQ R1 (1) -9145914672239476017->-8076412911421071267 -9145914672239476017->-3799845014019419063 8543938201983851330 chip.pool_ta_ctl -3219601238344183253 TAG-ALIGN 8543938201983851330->-3219601238344183253 -3219601238344183253->7826884721671710988 -3219601238344183253->-4392080887455103667 -3219601238344183253->-8121313071353540249 -3219601238344183253->302008383341661453 -3219601238344183253->6500479434923217917 -3219601238344183253->1529647233907073739 -3219601238344183253->6112888275474714771 -3219601238344183253->-4931438000231078795 -3219601238344183253->-3582356986900019706 -3219601238344183253->-4714068378521426992 -6752113594710268046 chip.bam2ta_ctl 1059970754191517209 TAG-ALIGN -6752113594710268046->1059970754191517209 1059970754191517209->-8121313071353540249 1059970754191517209->302008383341661453 1059970754191517209->6500479434923217917 1059970754191517209->1529647233907073739 1059970754191517209->8543938201983851330 1059970754191517209->-4931438000231078795 1059970754191517209->-3582356986900019706 -1709508556319356829 chip.filter_ctl 4766226206926994178 SAMstats QC -1709508556319356829->4766226206926994178 7914473835002812167 Filt/deduped BAM -1709508556319356829->7914473835002812167 7982001275543020932 LibCmplx QC -1709508556319356829->7982001275543020932 7914473835002812167->-6752113594710268046 7914473835002812167->-8893690107086681214 2311558002567337325 chip.align_ctl 3748739883952763072 SAMstats QC 2311558002567337325->3748739883952763072 -2315230606052893813 BAM 2311558002567337325->-2315230606052893813 -2315230606052893813->-1709508556319356829 -3359786550460631918 FASTQ R1 (1) -3359786550460631918->2311558002567337325 -9131231156078171852 chip.bam2ta_ctl 663811732337963577 TAG-ALIGN -9131231156078171852->663811732337963577 663811732337963577->-8121313071353540249 663811732337963577->302008383341661453 663811732337963577->6500479434923217917 663811732337963577->1529647233907073739 663811732337963577->8543938201983851330 663811732337963577->-4931438000231078795 663811732337963577->-3582356986900019706 -8744792186784332988 chip.filter_ctl 5413890298014519795 SAMstats QC -8744792186784332988->5413890298014519795 -3788243729033509246 Filt/deduped BAM -8744792186784332988->-3788243729033509246 43350535856486640 LibCmplx QC -8744792186784332988->43350535856486640 -3788243729033509246->-9131231156078171852 -3788243729033509246->-8893690107086681214 -7626786139367660132 chip.align_ctl -485592898538352319 BAM -7626786139367660132->-485592898538352319 -8090659142092204214 SAMstats QC -7626786139367660132->-8090659142092204214 -485592898538352319->-8744792186784332988 3216519453197460216 FASTQ R1 (1) 3216519453197460216->-7626786139367660132 -207950526549869804 IDR Plot ppr 6112888275474714771->-207950526549869804 -182359573568612196 IDR Peak ppr 6112888275474714771->-182359573568612196 -182359573568612196->-3582356986900019706 4949088101792782180 IDR Plot rep1_vs_rep2 5427617540906612683->4949088101792782180 -6745025974221474233 IDR NPeak rep1_vs_rep2 5427617540906612683->-6745025974221474233 -6745025974221474233->-3582356986900019706 6410801775414197522 Overlap Peak rep1_vs_rep2 2246475207573981792->6410801775414197522 6410801775414197522->-4931438000231078795 -3540716964904924958 Overlap Peak optimal -4931438000231078795->-3540716964904924958 1969459843590662807 Overlap reproducibility -4931438000231078795->1969459843590662807 3346766493950390484 IDR Peak optimal -3582356986900019706->3346766493950390484 -4431789579772618828 IDR reproducibility -3582356986900019706->-4431789579772618828 3766714205589023197 Overlap Peak ppr -4714068378521426992->3766714205589023197 3766714205589023197->-4931438000231078795 -2440437876574166281 JSD Plot -8893690107086681214->-2440437876574166281

UCSC browser tracks

UCSC track hub plain text 
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