File table
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FilesPath
Alignment
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/pooled-rep/pseudorep1/rep-pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/pooled-rep/pseudorep2/rep-pr2.pooled.tagAlign.gz
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/pooled-rep/rep.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.tagAlign.gz
Filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.bam
Raw BAM from aligner/users/leepc12/code/croo/examples/demo/run/atac/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.bam
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.tagAlign.gz
Filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.bam
Raw BAM from aligner/users/leepc12/code/croo/examples/demo/run/atac/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.bam
TAG-ALIGN/users/leepc12/code/croo/examples/demo/run/atac/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peak/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peak/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peak/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.starch
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered IDR peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.starch
Blacklist-filtered overlap peak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.starch
Unthresholded raw IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.gz
Pooled replicate
Pseudoreplicate 1
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep1/rep-pr1.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep1/rep-pr1.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep1/rep-pr1.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep1/rep-pr1.pooled.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep1/rep-pr1.pooled.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep2/rep-pr2.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep2/rep-pr2.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep2/rep-pr2.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep2/rep-pr2.pooled.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/pseudorep2/rep-pr2.pooled.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/rep.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/rep.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/rep.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/rep.pooled.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/pooled-rep/rep.pooled.pval0.01.300K.narrowPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered IDR peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.starch
Blacklist-filtered overlap peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.starch
Unthresholded raw IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.gz
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered IDR peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.starch
Blacklist-filtered overlap peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.starch
Unthresholded raw IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.narrowPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered IDR peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.starch
Blacklist-filtered overlap peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.starch
Unthresholded raw IDR peak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeak/users/leepc12/code/croo/examples/demo/run/atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.narrowPeak.gz
QC and logs
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/users/leepc12/code/croo/examples/demo/run/atac/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/users/leepc12/code/croo/examples/demo/run/atac/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/users/leepc12/code/croo/examples/demo/run/atac/qc/pooled-rep/pseudorep1/rep-pr1.pooled.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/pooled-rep/pseudorep2/rep-pr2.pooled.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/pooled-rep/rep.pooled.pval0.01.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/users/leepc12/code/croo/examples/demo/run/atac/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/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.frip.qc
Cross-correlation Plot/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.filt.no_chrM_MT.tn5.no_chrM.R1.25M.cc.plot.png
Cross-correlation score/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.filt.no_chrM_MT.tn5.no_chrM.R1.25M.cc.qc
Dup QC for filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.dup.qc
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.dupmark.lib_complexity.qc
Read length/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.read_length.txt
SAMstats log for Raw BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.samstats.qc
SAMstats log for filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.frip.qc
Cross-correlation Plot/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.filt.no_chrM_MT.tn5.no_chrM.R1.25M.cc.plot.png
Cross-correlation score/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.filt.no_chrM_MT.tn5.no_chrM.R1.25M.cc.qc
Dup QC for filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.dup.qc
Fraction of peaks in reads/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.dupmark.lib_complexity.qc
Read length/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.read_length.txt
SAMstats log for Raw BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.samstats.qc
SAMstats log for filtered BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.samstats.qc
Final HTML report/users/leepc12/code/croo/examples/demo/run/atac/qc/qc.html
Final QC JSON file/users/leepc12/code/croo/examples/demo/run/atac/qc/qc.json
Fraction of mitochondrial reads in raw BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/ENCFF341MYG.subsampled.400.trim.merged.srt.no_chrM.samstats.qc.frac_mito.qc
Fraction of mitochondrial reads in raw BAM/users/leepc12/code/croo/examples/demo/run/atac/qc/ENCFF641SFZ.subsampled.400.trim.merged.srt.no_chrM.samstats.qc.frac_mito.qc
Jensen-Shannon distance plot/users/leepc12/code/croo/examples/demo/run/atac/qc/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.jsd_plot.png
Reproducibility QC for IDR peaks/users/leepc12/code/croo/examples/demo/run/atac/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/users/leepc12/code/croo/examples/demo/run/atac/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/users/leepc12/code/croo/examples/demo/run/atac/signal/pooled-rep/rep.pooled.fc.signal.bigwig
MACS2 signal track (p-val)/users/leepc12/code/croo/examples/demo/run/atac/signal/pooled-rep/rep.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)/users/leepc12/code/croo/examples/demo/run/atac/signal/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.fc.signal.bigwig
MACS2 signal track (p-val)/users/leepc12/code/croo/examples/demo/run/atac/signal/rep1/ENCFF341MYG.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/users/leepc12/code/croo/examples/demo/run/atac/signal/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.fc.signal.bigwig
MACS2 signal track (p-val)/users/leepc12/code/croo/examples/demo/run/atac/signal/rep2/ENCFF641SFZ.subsampled.400.trim.merged.srt.nodup.no_chrM_MT.tn5.pval.signal.bigwig
Task graph
D cluster_pooled_rep Pooled replicate cluster_rep1 Replicate 1 cluster_rep2 Replicate 2 -2274614834825405594 pool_ta 1230005893615912661 TAG-ALIGN -2274614834825405594->1230005893615912661 -2790380951148322672 macs2_signal_track_pooled 1230005893615912661->-2790380951148322672 -2950461107855549355 call_peak_pooled 1230005893615912661->-2950461107855549355 -3082333051600846273 overlap 1230005893615912661->-3082333051600846273 -3672967665400115180 idr 1230005893615912661->-3672967665400115180 8596882385115866674 overlap_ppr 1230005893615912661->8596882385115866674 1660151472314774605 idr_ppr 1230005893615912661->1660151472314774605 7347663759321925507 BW FC -2790380951148322672->7347663759321925507 -1215741837334299082 BW p-val -2790380951148322672->-1215741837334299082 -3258311884937678782 Peak (bfilt) -2950461107855549355->-3258311884937678782 -1953143659675261813 Peak -2950461107855549355->-1953143659675261813 -1953143659675261813->-3082333051600846273 -1953143659675261813->-3672967665400115180 -1953143659675261813->8596882385115866674 -1953143659675261813->1660151472314774605 543441489586740213 bam2ta -4490259879637986529 TAG-ALIGN 543441489586740213->-4490259879637986529 -4490259879637986529->-2274614834825405594 3876800948215942389 macs2_signal_track -4490259879637986529->3876800948215942389 5227465817657782955 call_peak -4490259879637986529->5227465817657782955 5359966146201343249 reproducibility_overlap -4490259879637986529->5359966146201343249 -8881673304070790177 reproducibility_idr -4490259879637986529->-8881673304070790177 -4490259879637986529->8596882385115866674 -4490259879637986529->1660151472314774605 6993457229072215951 BW FC 3876800948215942389->6993457229072215951 8804321608315965156 BW p-val 3876800948215942389->8804321608315965156 -8440756912788017042 Peak (bfilt) 5227465817657782955->-8440756912788017042 -6396608661540495073 Peak 5227465817657782955->-6396608661540495073 -6396608661540495073->5359966146201343249 -6396608661540495073->-8881673304070790177 -6396608661540495073->-3082333051600846273 -6396608661540495073->-3672967665400115180 -2312979130321185487 filter -4739158440760495049 SAMstats QC -2312979130321185487->-4739158440760495049 7932827669093954780 Filt/deduped BAM -2312979130321185487->7932827669093954780 3383201765059420646 LibCmplx QC -2312979130321185487->3383201765059420646 7932827669093954780->543441489586740213 2156916957630363179 jsd 7932827669093954780->2156916957630363179 -564209889755748100 align 3591387331224312011 SAMstats QC -564209889755748100->3591387331224312011 -3892964299660623933 BAM -564209889755748100->-3892964299660623933 -3892964299660623933->-2312979130321185487 8371236509601150301 xcor -3892964299660623933->8371236509601150301 2746676891637925990 XCOR Plot 8371236509601150301->2746676891637925990 4190358650919371312 FASTQ R1 (1) 4190358650919371312->-564209889755748100 -6139964884720509797 FASTQ R1 (2) -6139964884720509797->-564209889755748100 3120151944654282671 FASTQ R2 (1) 3120151944654282671->-564209889755748100 3994318837471015312 FASTQ R2 (2) 3994318837471015312->-564209889755748100 -5070324449111802426 bam2ta 4689744713617676306 TAG-ALIGN -5070324449111802426->4689744713617676306 4689744713617676306->-2274614834825405594 3171746890110184227 macs2_signal_track 4689744713617676306->3171746890110184227 -5734957429915387360 call_peak 4689744713617676306->-5734957429915387360 4689744713617676306->5359966146201343249 4689744713617676306->-8881673304070790177 4689744713617676306->8596882385115866674 4689744713617676306->1660151472314774605 1467605807149282815 BW FC 3171746890110184227->1467605807149282815 7377506426059093217 BW p-val 3171746890110184227->7377506426059093217 6522526034113558929 Peak (bfilt) -5734957429915387360->6522526034113558929 1969103184955555543 Peak -5734957429915387360->1969103184955555543 1969103184955555543->5359966146201343249 1969103184955555543->-8881673304070790177 1969103184955555543->-3082333051600846273 1969103184955555543->-3672967665400115180 -3950948923124556421 filter 407172932136844799 SAMstats QC -3950948923124556421->407172932136844799 -1330041872742727701 Filt/deduped BAM -3950948923124556421->-1330041872742727701 -3694025367190381115 LibCmplx QC -3950948923124556421->-3694025367190381115 -1330041872742727701->-5070324449111802426 -1330041872742727701->2156916957630363179 -8754181613542316974 align 1870712359121339397 SAMstats QC -8754181613542316974->1870712359121339397 -176309796180252010 BAM -8754181613542316974->-176309796180252010 -176309796180252010->-3950948923124556421 8230883070733982408 xcor -176309796180252010->8230883070733982408 -2559063802149234091 XCOR Plot 8230883070733982408->-2559063802149234091 -1670650396220271743 FASTQ R1 (1) -1670650396220271743->-8754181613542316974 3494741633887347579 FASTQ R1 (2) 3494741633887347579->-8754181613542316974 -9042655555522006121 FASTQ R1 (3) -9042655555522006121->-8754181613542316974 -1099237758162680807 FASTQ R1 (4) -1099237758162680807->-8754181613542316974 8314128069893055732 FASTQ R1 (5) 8314128069893055732->-8754181613542316974 -270448024992318957 FASTQ R1 (6) -270448024992318957->-8754181613542316974 2517255272317529230 FASTQ R2 (1) 2517255272317529230->-8754181613542316974 -6432594655650054233 FASTQ R2 (2) -6432594655650054233->-8754181613542316974 3457585165415098216 FASTQ R2 (3) 3457585165415098216->-8754181613542316974 2305016322347271982 FASTQ R2 (4) 2305016322347271982->-8754181613542316974 6726896592449750873 FASTQ R2 (5) 6726896592449750873->-8754181613542316974 2200066227172172785 FASTQ R2 (6) 2200066227172172785->-8754181613542316974 -2191268334531194089 JSD Plot 2156916957630363179->-2191268334531194089 163167870719441504 Overlap Peak optimal 5359966146201343249->163167870719441504 -4577595377264280635 Overlap reproducibility 5359966146201343249->-4577595377264280635 7888972219552244141 IDR Peak optimal -8881673304070790177->7888972219552244141 6100658613509018840 IDR reproducibility -8881673304070790177->6100658613509018840 1484377438019781702 Overlap Peak rep1_vs_rep2 -3082333051600846273->1484377438019781702 1484377438019781702->5359966146201343249 -5134912485975395331 IDR Plot rep1_vs_rep2 -3672967665400115180->-5134912485975395331 -8582485590420767 IDR NPeak rep1_vs_rep2 -3672967665400115180->-8582485590420767 -8582485590420767->-8881673304070790177 987277693701275511 Overlap Peak ppr 8596882385115866674->987277693701275511 987277693701275511->5359966146201343249 -4239262811553911260 IDR Plot ppr 1660151472314774605->-4239262811553911260 -2571580602055613407 IDR Peak ppr 1660151472314774605->-2571580602055613407 -2571580602055613407->-8881673304070790177