File table
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FilesPath
Alignment
Control 1
Filtered BAMgs://encode-pipeline-output-definition/out_example_chip/align/ctl1/ctl1-R1.subsampled.80.merged.nodup.bam
Raw BAM from bwags://encode-pipeline-output-definition/out_example_chip/align/ctl1/ctl1-R1.subsampled.80.merged.bam
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/ctl1/ctl1-R1.subsampled.80.merged.nodup.tagAlign.gz
Control 2
Filtered BAMgs://encode-pipeline-output-definition/out_example_chip/align/ctl2/ctl2-R1.subsampled.80.merged.nodup.bam
Raw BAM from bwags://encode-pipeline-output-definition/out_example_chip/align/ctl2/ctl2-R1.subsampled.80.merged.bam
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/ctl2/ctl2-R1.subsampled.80.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/pooled-ctl/ctl1-R1.subsampled.80.merged.nodup.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/pooled-rep/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/pooled-rep/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2.pooled.tagAlign.gz
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/rep1/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/rep1/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-output-definition/out_example_chip/align/rep1/rep1-R1.subsampled.67.merged.nodup.bam
Raw BAM from bwags://encode-pipeline-output-definition/out_example_chip/align/rep1/rep1-R1.subsampled.67.merged.bam
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/rep1/rep1-R1.subsampled.67.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/rep2/pseudorep1/rep2-R1.subsampled.67.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/rep2/pseudorep2/rep2-R1.subsampled.67.merged.nodup.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-output-definition/out_example_chip/align/rep2/rep2-R1.subsampled.67.merged.nodup.bam
Raw BAM from bwags://encode-pipeline-output-definition/out_example_chip/align/rep2/rep2-R1.subsampled.67.merged.bam
TAG-ALIGNgs://encode-pipeline-output-definition/out_example_chip/align/rep2/rep2-R1.subsampled.67.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://encode-pipeline-output-definition/out_example_chip/peak/idr_reproducibility/conservative_peak.regionPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/idr_reproducibility/conservative_peak.regionPeak.bb
Optimal peakgs://encode-pipeline-output-definition/out_example_chip/peak/idr_reproducibility/optimal_peak.regionPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/idr_reproducibility/optimal_peak.regionPeak.bb
Overlap reproducibility
Conservative peakgs://encode-pipeline-output-definition/out_example_chip/peak/overlap_reproducibility/conservative_peak.regionPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/overlap_reproducibility/conservative_peak.regionPeak.bb
Optimal peakgs://encode-pipeline-output-definition/out_example_chip/peak/overlap_reproducibility/optimal_peak.regionPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/overlap_reproducibility/optimal_peak.regionPeak.bb
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.regionPeak.bb
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-pseudorep1_vs_2/ppr.idr0.05.unthresholded-peaks.txt.gz
Pooled replicate
Pseudoreplicate 1
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.regionPeak.gz
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.pval0.01.500K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.pval0.01.500K.bfilt.narrowPeak.bb
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.pval0.01.500K.narrowPeak.gz
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1_vs_rep2/rep1_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1_vs_rep2/rep1_rep2.overlap.bfilt.regionPeak.bb
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_chip/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_chip/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.regionPeak.bb
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.pval0.01.500K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.pval0.01.500K.bfilt.narrowPeak.bb
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.pval0.01.500K.narrowPeak.gz
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.300K.regionPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered overlap peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.regionPeak.bb
Unthresholded raw IDR peakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/pseudorep1/rep2-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep2/pseudorep1/rep2-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/pseudorep1/rep2-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/pseudorep2/rep2-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep2/pseudorep2/rep2-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/pseudorep2/rep2-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.pval0.01.500K.bfilt.narrowPeak.gz
Blacklist-filtered MACS2 narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.pval0.01.500K.bfilt.narrowPeak.bb
Blacklist-filtered SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered SPP narrowpeak (BigBed)gs://encode-pipeline-output-definition/out_example_chip/peak/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Raw MACS2 narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.pval0.01.500K.narrowPeak.gz
Raw SPP narrowpeakgs://encode-pipeline-output-definition/out_example_chip/peak/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl1/ctl1-R1.subsampled.80.merged.dup.qc
PBC QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl1/ctl1-R1.subsampled.80.merged.dupmark.pbc.qc
Samtools flagstat for Raw BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl1/ctl1-R1.subsampled.80.merged.flagstat.qc
Samtools flagstat log for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl1/ctl1-R1.subsampled.80.merged.nodup.flagstat.qc
Control 2
Dup QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl2/ctl2-R1.subsampled.80.merged.dup.qc
PBC QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl2/ctl2-R1.subsampled.80.merged.dupmark.pbc.qc
Samtools flagstat for Raw BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl2/ctl2-R1.subsampled.80.merged.flagstat.qc
Samtools flagstat log for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/ctl2/ctl2-R1.subsampled.80.merged.nodup.flagstat.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-pseudorep1_vs_2/ppr.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-pseudorep1_vs_2/ppr.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_chip/qc/pooled-pseudorep1_vs_2/ppr.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-pseudorep1_vs_2/ppr.idr0.05.unthresholded-peaks.txt.png
Pooled replicate
Pseudoreplicate 1
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-rep/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-rep/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.frip.qc
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.pval0.01.500K.bfilt.frip.qc
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.frip.qc
Rep1 vs. rep2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1_vs_rep2/rep1_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1_vs_rep2/rep1_rep2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_chip/qc/rep1_vs_rep2/rep1_rep2.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_chip/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_chip/qc/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1-pseudorep1_vs_2/rep1-pr.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_chip/qc/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_chip/qc/rep1-pseudorep1_vs_2/rep1-pr.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/pseudorep1/rep1-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/pseudorep2/rep1-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plotgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.trim_50bp.no_chrM.15M.cc.plot.png
Cross-correlation scoregs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.trim_50bp.no_chrM.15M.cc.qc
Dup QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.dup.qc
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.pval0.01.500K.bfilt.frip.qc
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
PBC QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.dupmark.pbc.qc
Samtools flagstat for Raw BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.flagstat.qc
Samtools flagstat log for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep1/rep1-R1.subsampled.67.merged.nodup.flagstat.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep2-pseudorep1_vs_2/rep2-pr.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-output-definition/out_example_chip/qc/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.log
IDR plotgs://encode-pipeline-output-definition/out_example_chip/qc/rep2-pseudorep1_vs_2/rep2-pr.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/pseudorep1/rep2-R1.subsampled.67.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/pseudorep2/rep2-R1.subsampled.67.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plotgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.trim_50bp.no_chrM.15M.cc.plot.png
Cross-correlation scoregs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.trim_50bp.no_chrM.15M.cc.qc
Dup QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.dup.qc
Fraction of MACS2 peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.pval0.01.500K.bfilt.frip.qc
Fraction of SPP peaks in readsgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
PBC QC for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.dupmark.pbc.qc
Samtools flagstat for Raw BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.flagstat.qc
Samtools flagstat log for filtered BAMgs://encode-pipeline-output-definition/out_example_chip/qc/rep2/rep2-R1.subsampled.67.merged.nodup.flagstat.qc
Deeptools fingerprint plotgs://encode-pipeline-output-definition/out_example_chip/qc/rep1-R1.subsampled.67.merged.nodup.jsd_plot.png
Final HTML reportgs://encode-pipeline-output-definition/out_example_chip/qc/qc.html
Final QC JSON filegs://encode-pipeline-output-definition/out_example_chip/qc/qc.json
Reproducibility QC for IDR peaksgs://encode-pipeline-output-definition/out_example_chip/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://encode-pipeline-output-definition/out_example_chip/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)gs://encode-pipeline-output-definition/out_example_chip/signal/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-output-definition/out_example_chip/signal/pooled-rep/rep1-R1.subsampled.67.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)gs://encode-pipeline-output-definition/out_example_chip/signal/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-output-definition/out_example_chip/signal/rep1/rep1-R1.subsampled.67.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)gs://encode-pipeline-output-definition/out_example_chip/signal/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-output-definition/out_example_chip/signal/rep2/rep2-R1.subsampled.67.merged.nodup_x_ctl_for_rep2.pval.signal.bigwig