File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/pe/align/ctl1/ctl1-R1.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/pe/align/ctl1/ctl1-R1.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/ctl1/ctl1-R1.merged.nodup.tagAlign.gz
Control 2
Filtered BAM/srv/www/kundaje/natprot_chip/pe/align/ctl2/ctl2-R1.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/pe/align/ctl2/ctl2-R1.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/ctl2/ctl2-R1.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/pooled-ctl/ctl1-R1.merged.nodup.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/pooled-rep/pseudorep1/rep1-R1.merged.nodup.pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/pooled-rep/pseudorep2/rep1-R1.merged.nodup.pr2.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/pooled-rep/rep1-R1.merged.nodup.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/rep1/pseudorep1/rep1-R1.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/rep1/pseudorep2/rep1-R1.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/pe/align/rep1/rep1-R1.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/pe/align/rep1/rep1-R1.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/rep1/rep1-R1.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/rep2/pseudorep1/rep2-R1.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/rep2/pseudorep2/rep2-R1.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/pe/align/rep2/rep2-R1.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/pe/align/rep2/rep2-R1.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/pe/align/rep2/rep2-R1.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/pe/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/pe/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/pe/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/pe/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/pe/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/pe/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/pe/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/pe/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/pe/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/pe/peak/pooled-rep/pseudorep1/rep1-R1.merged.nodup.pr1.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep1/rep1-R1.merged.nodup.pr1.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep1/rep1-R1.merged.nodup.pr1.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep1/rep1-R1.merged.nodup.pr1.pooled_x_ctl1-R1.merged.nodup.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep2/rep1-R1.merged.nodup.pr2.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep2/rep1-R1.merged.nodup.pr2.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep2/rep1-R1.merged.nodup.pr2.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/pseudorep2/rep1-R1.merged.nodup.pr2.pooled_x_ctl1-R1.merged.nodup.pooled.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/pe/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/pe/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/pe/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/pe/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/pe/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/pe/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/pe/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/pe/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/pe/peak/rep1/pseudorep1/rep1-R1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep1/rep1-R1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep1/rep1-R1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep1/rep1-R1.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep2/rep1-R1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep2/rep1-R1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep2/rep1-R1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep1/pseudorep2/rep1-R1.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep1/rep1-R1.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep1/rep1-R1.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep1/rep1-R1.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep1/rep1-R1.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/pe/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/pe/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/pe/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/pe/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/pe/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/pe/peak/rep2/pseudorep1/rep2-R1.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep1/rep2-R1.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep1/rep2-R1.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep1/rep2-R1.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep2/rep2-R1.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep2/rep2-R1.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep2/rep2-R1.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep2/pseudorep2/rep2-R1.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep2/rep2-R1.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/pe/peak/rep2/rep2-R1.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/pe/peak/rep2/rep2-R1.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/pe/peak/rep2/rep2-R1.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl1/ctl1-R1.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl1/ctl1-R1.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl1/ctl1-R1.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl1/ctl1-R1.merged.nodup.samstats.qc
Control 2
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl2/ctl2-R1.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl2/ctl2-R1.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl2/ctl2-R1.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/ctl2/ctl2-R1.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/pe/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/pe/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/pe/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/pe/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/pe/qc/pooled-rep/pseudorep1/rep1-R1.merged.nodup.pr1.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/pooled-rep/pseudorep2/rep1-R1.merged.nodup.pr2.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.frip.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/pe/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/pe/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/pe/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/pe/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/pe/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/pe/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/pe/qc/rep1/pseudorep1/rep1-R1.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/rep1/pseudorep2/rep1-R1.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/rep1/rep1-R1.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/pe/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/pe/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/pe/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/pe/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/pe/qc/rep2/pseudorep1/rep2-R1.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/rep2/pseudorep2/rep2-R1.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/pe/qc/rep2/rep2-R1.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/pe/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/pe/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/pe/qc/rep1-R1.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/pe/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/pe/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/pe/signal/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/pe/signal/pooled-rep/rep1-R1.merged.nodup.pooled_x_ctl1-R1.merged.nodup.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/pe/signal/rep1/rep1-R1.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/pe/signal/rep1/rep1-R1.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/pe/signal/rep2/rep2-R1.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/pe/signal/rep2/rep2-R1.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 5836596448738223052 chip.macs2_signal_track_pooled 4791478994923230637 BW p-val 5836596448738223052->4791478994923230637 -8843756195521399145 BW FC 5836596448738223052->-8843756195521399145 7033099943519060825 chip.call_peak_pooled 8560296423847511427 Peak (bfilt) 7033099943519060825->8560296423847511427 -6294455469262471943 Peak 7033099943519060825->-6294455469262471943 1706143195554342159 chip.idr_ppr -6294455469262471943->1706143195554342159 -1847868203846317464 chip.idr -6294455469262471943->-1847868203846317464 -8438044255287477198 chip.overlap -6294455469262471943->-8438044255287477198 6085990846400089692 chip.overlap_ppr -6294455469262471943->6085990846400089692 4979069162830568717 chip.pool_ta -3293253196568039207 TAG-ALIGN 4979069162830568717->-3293253196568039207 -3293253196568039207->5836596448738223052 -3293253196568039207->7033099943519060825 -3457735636362203891 chip.call_peak -3293253196568039207->-3457735636362203891 -7398949305557754487 chip.macs2_signal_track -3293253196568039207->-7398949305557754487 -59772032189414787 chip.call_peak -3293253196568039207->-59772032189414787 3732600712637901992 chip.macs2_signal_track -3293253196568039207->3732600712637901992 -3293253196568039207->1706143195554342159 -3293253196568039207->-1847868203846317464 -3293253196568039207->-8438044255287477198 4032368116197483646 chip.reproducibility_overlap -3293253196568039207->4032368116197483646 8726836172449964070 chip.reproducibility_idr -3293253196568039207->8726836172449964070 -3293253196568039207->6085990846400089692 2312997050099273475 Peak (bfilt) -3457735636362203891->2312997050099273475 1282723735600343982 Peak -3457735636362203891->1282723735600343982 1282723735600343982->-1847868203846317464 1282723735600343982->-8438044255287477198 1282723735600343982->4032368116197483646 1282723735600343982->8726836172449964070 8622868263362206580 chip.bam2ta -4015849846061652293 TAG-ALIGN 8622868263362206580->-4015849846061652293 -4015849846061652293->4979069162830568717 -4015849846061652293->-3457735636362203891 -4015849846061652293->-7398949305557754487 -4015849846061652293->-59772032189414787 -4015849846061652293->3732600712637901992 -4015849846061652293->1706143195554342159 -4015849846061652293->4032368116197483646 -4015849846061652293->8726836172449964070 -4015849846061652293->6085990846400089692 3222664562077657571 chip.filter -6788955765518074577 SAMstats QC 3222664562077657571->-6788955765518074577 4528241812767474523 Filt/deduped BAM 3222664562077657571->4528241812767474523 -4050721800203237012 LibCmplx QC 3222664562077657571->-4050721800203237012 4528241812767474523->8622868263362206580 -7446474058711324841 chip.jsd 4528241812767474523->-7446474058711324841 4939116212136609633 chip.align -501998316273997665 SAMstats QC 4939116212136609633->-501998316273997665 4307916683098179385 BAM 4939116212136609633->4307916683098179385 4307916683098179385->3222664562077657571 -8445435763282948257 chip.xcor 1295191068862699183 XCOR Plot -8445435763282948257->1295191068862699183 2869956355486074570 BW p-val -7398949305557754487->2869956355486074570 -6226655123782158930 BW FC -7398949305557754487->-6226655123782158930 3352409701192572420 FASTQ R1 (1) 3352409701192572420->4939116212136609633 3352409701192572420->-8445435763282948257 959960066710237547 FASTQ R2 (1) 959960066710237547->4939116212136609633 4247913694085193685 Peak (bfilt) -59772032189414787->4247913694085193685 -3822450384285225052 Peak -59772032189414787->-3822450384285225052 -3822450384285225052->-1847868203846317464 -3822450384285225052->-8438044255287477198 -3822450384285225052->4032368116197483646 -3822450384285225052->8726836172449964070 2899186673507598021 chip.bam2ta 4705128800388592341 TAG-ALIGN 2899186673507598021->4705128800388592341 4705128800388592341->4979069162830568717 4705128800388592341->-3457735636362203891 4705128800388592341->-7398949305557754487 4705128800388592341->-59772032189414787 4705128800388592341->3732600712637901992 4705128800388592341->1706143195554342159 4705128800388592341->4032368116197483646 4705128800388592341->8726836172449964070 4705128800388592341->6085990846400089692 1189158948797844708 chip.filter 1545988608075469009 SAMstats QC 1189158948797844708->1545988608075469009 8094894187214183871 Filt/deduped BAM 1189158948797844708->8094894187214183871 -5338345815165942640 LibCmplx QC 1189158948797844708->-5338345815165942640 8094894187214183871->2899186673507598021 8094894187214183871->-7446474058711324841 5434227271862435603 chip.align 2183056063264133508 SAMstats QC 5434227271862435603->2183056063264133508 -5914043081930408282 BAM 5434227271862435603->-5914043081930408282 -5914043081930408282->1189158948797844708 -1242593810592451494 chip.xcor 4754264210331488483 XCOR Plot -1242593810592451494->4754264210331488483 -1030336998594873536 BW FC 3732600712637901992->-1030336998594873536 -6422693960780004182 BW p-val 3732600712637901992->-6422693960780004182 -8327015267994400103 FASTQ R1 (1) -8327015267994400103->5434227271862435603 -8327015267994400103->-1242593810592451494 277070679238412866 FASTQ R2 (1) 277070679238412866->5434227271862435603 7797264777723342661 chip.pool_ta_ctl 6037175730513825397 TAG-ALIGN 7797264777723342661->6037175730513825397 6037175730513825397->5836596448738223052 6037175730513825397->7033099943519060825 6037175730513825397->-3457735636362203891 6037175730513825397->-7398949305557754487 6037175730513825397->-59772032189414787 6037175730513825397->3732600712637901992 6037175730513825397->1706143195554342159 6037175730513825397->4032368116197483646 6037175730513825397->8726836172449964070 6037175730513825397->6085990846400089692 9162933104325955094 chip.bam2ta_ctl -7984629060827029500 TAG-ALIGN 9162933104325955094->-7984629060827029500 -7984629060827029500->-3457735636362203891 -7984629060827029500->-7398949305557754487 -7984629060827029500->-59772032189414787 -7984629060827029500->3732600712637901992 -7984629060827029500->7797264777723342661 -7984629060827029500->4032368116197483646 -7984629060827029500->8726836172449964070 -8486308040121451015 chip.filter_ctl 6789428637581494397 SAMstats QC -8486308040121451015->6789428637581494397 -6732299266197949179 Filt/deduped BAM -8486308040121451015->-6732299266197949179 -4346966586646719489 LibCmplx QC -8486308040121451015->-4346966586646719489 -6732299266197949179->9162933104325955094 -6732299266197949179->-7446474058711324841 6639806394933856448 chip.align_ctl 3547498868926897243 BAM 6639806394933856448->3547498868926897243 5842576732167131756 SAMstats QC 6639806394933856448->5842576732167131756 3547498868926897243->-8486308040121451015 -1517011488090641209 FASTQ R1 (1) -1517011488090641209->6639806394933856448 7251394286446648806 FASTQ R2 (1) 7251394286446648806->6639806394933856448 7823865927269536153 chip.bam2ta_ctl -3463690884392319952 TAG-ALIGN 7823865927269536153->-3463690884392319952 -3463690884392319952->-3457735636362203891 -3463690884392319952->-7398949305557754487 -3463690884392319952->-59772032189414787 -3463690884392319952->3732600712637901992 -3463690884392319952->7797264777723342661 -3463690884392319952->4032368116197483646 -3463690884392319952->8726836172449964070 7487469589264556440 chip.filter_ctl -962496023978628782 SAMstats QC 7487469589264556440->-962496023978628782 -7661900427418860983 Filt/deduped BAM 7487469589264556440->-7661900427418860983 -692743583488235745 LibCmplx QC 7487469589264556440->-692743583488235745 -7661900427418860983->7823865927269536153 -7661900427418860983->-7446474058711324841 -6579817187313151752 chip.align_ctl 6324225447194717712 SAMstats QC -6579817187313151752->6324225447194717712 -5674964343388451400 BAM -6579817187313151752->-5674964343388451400 -5674964343388451400->7487469589264556440 2918970993523822337 FASTQ R1 (1) 2918970993523822337->-6579817187313151752 4127601339169042265 FASTQ R2 (1) 4127601339169042265->-6579817187313151752 6610960842743741547 IDR Plot ppr 1706143195554342159->6610960842743741547 -8474644910297283528 IDR Peak ppr 1706143195554342159->-8474644910297283528 -8474644910297283528->8726836172449964070 -9022013274547525827 IDR Plot rep1_vs_rep2 -1847868203846317464->-9022013274547525827 8730601030793926769 IDR NPeak rep1_vs_rep2 -1847868203846317464->8730601030793926769 8730601030793926769->8726836172449964070 6290918393110862803 Overlap Peak rep1_vs_rep2 -8438044255287477198->6290918393110862803 6290918393110862803->4032368116197483646 5072136305010807786 Overlap Peak optimal 4032368116197483646->5072136305010807786 -7970121441413294727 Overlap reproducibility 4032368116197483646->-7970121441413294727 -3548295192792751599 IDR Peak optimal 8726836172449964070->-3548295192792751599 -3642826984746602178 IDR reproducibility 8726836172449964070->-3642826984746602178 -7836321266287657265 Overlap Peak ppr 6085990846400089692->-7836321266287657265 -7836321266287657265->4032368116197483646 -6166989174996170514 JSD Plot -7446474058711324841->-6166989174996170514

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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