File table
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FilesPath
Alignment
Pooled replicate
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pooled.tagAlign.gz
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.bam
Raw BAM from alignergs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.bam
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.bam
Raw BAM from alignergs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.bam
TAG-ALIGNgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Optimal peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Overlap reproducibility
Conservative peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Optimal peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.gz
Pooled replicate
Pseudoreplicate 1
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pooled.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pooled.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval0.01.300K.narrowPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.gz
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.narrowPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.narrowPeak.gz
QC and logs
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.png
Pooled replicate
Pseudoreplicate 1
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pooled.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pooled.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval0.01.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/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 readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.frip.qc
Dup QC for filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.dup.qc
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.frip.qc
Library complexity QC for filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.dupmark.lib_complexity.qc
Read lengthgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.read_length.txt
SAMstats log for Raw BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.samstats.qc
SAMstats log for filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pr2.pval0.01.300K.bfilt.frip.qc
Dup QC for filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.dup.qc
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.frip.qc
Library complexity QC for filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.dupmark.lib_complexity.qc
Read lengthgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.read_length.txt
SAMstats log for Raw BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.samstats.qc
SAMstats log for filtered BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.samstats.qc
Final HTML reportgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/qc.html
Final QC JSON filegs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/qc.json
Fraction of mitochondrial reads in raw BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/ENCFF341MYG.subsampled.400.trim.merged.no_chrM.samstats.qc.frac_mito.qc
Fraction of mitochondrial reads in raw BAMgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/ENCFF641SFZ.subsampled.400.trim.merged.no_chrM.samstats.qc.frac_mito.qc
Jensen-Shannon distance plotgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.jsd_plot.png
Reproducibility QC for IDR peaksgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/signal/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/signal/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/signal/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/signal/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/signal/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/croo_example/signal/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.no_chrM_MT.tn5.pval.signal.bigwig
Task graph D cluster_pooled_rep Pooled replicate cluster_rep1 Replicate 1 cluster_rep2 Replicate 2 3742098640264546264 atac.pool_ta -864199628318436445 TAG-ALIGN 3742098640264546264->-864199628318436445 -8694253705857038974 atac.macs2_signal_track_pooled -864199628318436445->-8694253705857038974 4651552189924851217 atac.call_peak_pooled -864199628318436445->4651552189924851217 -7589458644398994117 atac.overlap -864199628318436445->-7589458644398994117 8099996305320602396 atac.idr -864199628318436445->8099996305320602396 4386873339046245581 atac.overlap_ppr -864199628318436445->4386873339046245581 8320502365756997412 atac.idr_ppr -864199628318436445->8320502365756997412 5145582092083160897 BW p-val -8694253705857038974->5145582092083160897 -3986379230660313551 BW FC -8694253705857038974->-3986379230660313551 -6502237092843934915 Peak (bfilt) 4651552189924851217->-6502237092843934915 -6593251991145237235 Peak 4651552189924851217->-6593251991145237235 -6593251991145237235->-7589458644398994117 -6593251991145237235->8099996305320602396 -6593251991145237235->4386873339046245581 -6593251991145237235->8320502365756997412 -2580531364267789815 atac.bam2ta -1075899662783287678 TAG-ALIGN -2580531364267789815->-1075899662783287678 -1075899662783287678->3742098640264546264 -4244303147049366700 atac.macs2_signal_track -1075899662783287678->-4244303147049366700 4765036228314558778 atac.call_peak -1075899662783287678->4765036228314558778 -9186649410453825167 atac.reproducibility_overlap -1075899662783287678->-9186649410453825167 6578857324749572427 atac.reproducibility_idr -1075899662783287678->6578857324749572427 -1075899662783287678->4386873339046245581 -1075899662783287678->8320502365756997412 6875797360545150785 BW FC -4244303147049366700->6875797360545150785 -6055047103493112136 BW p-val -4244303147049366700->-6055047103493112136 -5940302578903923758 Peak (bfilt) 4765036228314558778->-5940302578903923758 2404627160419540389 Peak 4765036228314558778->2404627160419540389 2404627160419540389->-9186649410453825167 2404627160419540389->6578857324749572427 2404627160419540389->-7589458644398994117 2404627160419540389->8099996305320602396 -3362931993649702963 atac.filter -8978168337543142773 SAMstats QC -3362931993649702963->-8978168337543142773 -6036681552995554517 Filt/deduped BAM -3362931993649702963->-6036681552995554517 3499401798079034482 LibCmplx QC -3362931993649702963->3499401798079034482 -6036681552995554517->-2580531364267789815 -1537915438703024 atac.jsd -6036681552995554517->-1537915438703024 813793526239106131 atac.align 2831298477228633257 SAMstats QC 813793526239106131->2831298477228633257 -463754596993184070 BAM 813793526239106131->-463754596993184070 -463754596993184070->-3362931993649702963 -8293964782782343832 FASTQ R1 (1) -8293964782782343832->813793526239106131 2046107720969034781 FASTQ R1 (2) 2046107720969034781->813793526239106131 1029883486410880898 FASTQ R2 (1) 1029883486410880898->813793526239106131 7158875202846092280 FASTQ R2 (2) 7158875202846092280->813793526239106131 -460427452414210264 atac.bam2ta -2396834739825205626 TAG-ALIGN -460427452414210264->-2396834739825205626 -2396834739825205626->3742098640264546264 5453501538211985193 atac.macs2_signal_track -2396834739825205626->5453501538211985193 -8962436466869963662 atac.call_peak -2396834739825205626->-8962436466869963662 -2396834739825205626->-9186649410453825167 -2396834739825205626->6578857324749572427 -2396834739825205626->4386873339046245581 -2396834739825205626->8320502365756997412 -7511537389448999850 BW FC 5453501538211985193->-7511537389448999850 -2919321303501539506 BW p-val 5453501538211985193->-2919321303501539506 527851504113810164 Peak (bfilt) -8962436466869963662->527851504113810164 6782875770819416802 Peak -8962436466869963662->6782875770819416802 6782875770819416802->-9186649410453825167 6782875770819416802->6578857324749572427 6782875770819416802->-7589458644398994117 6782875770819416802->8099996305320602396 7789616136065539943 atac.filter 7834745771551401187 SAMstats QC 7789616136065539943->7834745771551401187 3074045854255555669 Filt/deduped BAM 7789616136065539943->3074045854255555669 -1801880376414787492 LibCmplx QC 7789616136065539943->-1801880376414787492 3074045854255555669->-460427452414210264 3074045854255555669->-1537915438703024 2747202979615198679 atac.align 4457644761936421903 SAMstats QC 2747202979615198679->4457644761936421903 -8586675476197336999 BAM 2747202979615198679->-8586675476197336999 -8586675476197336999->7789616136065539943 7523180718818791012 FASTQ R1 (1) 7523180718818791012->2747202979615198679 6425105801118140374 FASTQ R1 (2) 6425105801118140374->2747202979615198679 -3340343352839832947 FASTQ R1 (3) -3340343352839832947->2747202979615198679 4615694076038988196 FASTQ R1 (4) 4615694076038988196->2747202979615198679 -610810995796387489 FASTQ R1 (5) -610810995796387489->2747202979615198679 8445055260271957432 FASTQ R1 (6) 8445055260271957432->2747202979615198679 -6734248517944454648 FASTQ R2 (1) -6734248517944454648->2747202979615198679 7499797612071744878 FASTQ R2 (2) 7499797612071744878->2747202979615198679 -5775221591907480564 FASTQ R2 (3) -5775221591907480564->2747202979615198679 3850757442793103563 FASTQ R2 (4) 3850757442793103563->2747202979615198679 5058949744756336232 FASTQ R2 (5) 5058949744756336232->2747202979615198679 -340332416672361592 FASTQ R2 (6) -340332416672361592->2747202979615198679 5200349738161116893 JSD Plot -1537915438703024->5200349738161116893 1955785988417277759 Overlap Peak optimal -9186649410453825167->1955785988417277759 8571955851307854441 Overlap reproducibility -9186649410453825167->8571955851307854441 4802002033785585460 IDR Peak optimal 6578857324749572427->4802002033785585460 778646292734695238 IDR reproducibility 6578857324749572427->778646292734695238 -8032189922658688944 Overlap Peak rep1_vs_rep2 -7589458644398994117->-8032189922658688944 -8032189922658688944->-9186649410453825167 -4763545132020857334 IDR Plot rep1_vs_rep2 8099996305320602396->-4763545132020857334 8843568833286902350 IDR NPeak rep1_vs_rep2 8099996305320602396->8843568833286902350 8843568833286902350->6578857324749572427 -3803715463730469469 Overlap Peak ppr 4386873339046245581->-3803715463730469469 -3803715463730469469->-9186649410453825167 -5690929918355801006 IDR Plot ppr 8320502365756997412->-5690929918355801006 -6900752724629858352 IDR Peak ppr 8320502365756997412->-6900752724629858352 -6900752724629858352->6578857324749572427

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