File table
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FilesPath
Alignment
Pooled replicate
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pooled.tagAlign.gz
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-output-definition/out_example_atac/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam
Raw BAM from bowtie2gs://encode-pipeline-output-definition/out_example_atac/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.bam
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-output-definition/out_example_atac/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.bam
Raw BAM from bowtie2gs://encode-pipeline-output-definition/out_example_atac/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.bam
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_atac/align/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://encode-pipeline-output-definition/out_example_atac/peak/idr_reproducibility/conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/idr_reproducibility/conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/idr_reproducibility/conservative_peak.narrowPeak.hammock.gz
Optimal peakgs://encode-pipeline-output-definition/out_example_atac/peak/idr_reproducibility/optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/idr_reproducibility/optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/idr_reproducibility/optimal_peak.narrowPeak.hammock.gz
Overlap reproducibility
Conservative peakgs://encode-pipeline-output-definition/out_example_atac/peak/overlap_reproducibility/conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/overlap_reproducibility/conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/overlap_reproducibility/conservative_peak.narrowPeak.hammock.gz
Optimal peakgs://encode-pipeline-output-definition/out_example_atac/peak/overlap_reproducibility/optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/overlap_reproducibility/optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/overlap_reproducibility/optimal_peak.narrowPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.unthresholded-peaks.txt.gz
Pooled replicate
Pseudoreplicate 1
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pooled.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pooled.pval0.01.300K.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.pval0.01.300K.narrowPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1_vs_rep2/rep1_rep2.idr0.05.unthresholded-peaks.txt.gz
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.narrowPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.narrowPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered MACS2 narrowpeak (hammock)gs://encode-pipeline-output-definition/out_example_atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_atac/peak/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.narrowPeak.gz
QC and logs
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_atac/qc/pooled-pseudorep1_vs_2/ppr.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_atac/qc/pooled-pseudorep1_vs_2/ppr.idr0.05.unthresholded-peaks.txt.png
Pooled replicate
Pseudoreplicate 1
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/pooled-rep/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pooled.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/pooled-rep/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pooled.pval0.01.300K.bfilt.frip.qc
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.pval0.01.300K.bfilt.frip.qc
Rep1 vs. rep2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1_vs_rep2/rep1_rep2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_atac/qc/rep1_vs_rep2/rep1_rep2.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_atac/qc/rep1_vs_rep2/rep1_rep2.idr0.05.unthresholded-peaks.txt.png
Replicate 1
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_atac/qc/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_atac/qc/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/pseudorep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/pseudorep2/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.frip.qc
ATAqC summary reportgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged_qc.html
ATAqC summary txtgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged_qc.txt
Alignment log from bowtie2gs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.align.log
Cross-correlation Plotgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25M.cc.plot.png
Cross-correlation scoregs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25M.cc.qc
Dup QC for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.dup.qc
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.frip.qc
Mito dup log for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.dupmark.mito_dup.txt
PBC QC for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.dupmark.pbc.qc
Read lengthgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF248EJF.subsampled.400.trim.merged.read_length.txt
Samtools flagstat for Raw BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.flagstat.qc
Samtools flagstat log for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.flagstat.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_atac/qc/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_atac/qc/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/pseudorep1/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/pseudorep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pr2.pval0.01.300K.bfilt.frip.qc
ATAqC summary reportgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged_qc.html
ATAqC summary txtgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged_qc.txt
Alignment log from bowtie2gs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.align.log
Cross-correlation Plotgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25M.cc.plot.png
Cross-correlation scoregs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25M.cc.qc
Dup QC for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.dup.qc
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pval0.01.300K.bfilt.frip.qc
Mito dup log for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.dupmark.mito_dup.txt
PBC QC for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.dupmark.pbc.qc
Read lengthgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF031ARQ.subsampled.400.trim.merged.read_length.txt
Samtools flagstat for Raw BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.flagstat.qc
Samtools flagstat log for filtered BAMgs://encode-pipeline-output-definition/out_example_atac/qc/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.flagstat.qc
Final HTML reportgs://encode-pipeline-output-definition/out_example_atac/qc/qc.html
Final QC JSON filegs://encode-pipeline-output-definition/out_example_atac/qc/qc.json
Reproducibility QC for IDR peaksgs://encode-pipeline-output-definition/out_example_atac/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://encode-pipeline-output-definition/out_example_atac/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)gs://encode-pipeline-output-definition/out_example_atac/signal/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-output-definition/out_example_atac/signal/pooled-rep/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)gs://encode-pipeline-output-definition/out_example_atac/signal/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-output-definition/out_example_atac/signal/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)gs://encode-pipeline-output-definition/out_example_atac/signal/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-output-definition/out_example_atac/signal/rep2/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.pval.signal.bigwig