File table
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FilesPath
Alignment
Control 1
Filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/ctl1/ctl1-R1.subsampled.80.merged.nodup.bam
Raw BAM from alignergs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/ctl1/ctl1-R1.subsampled.80.merged.bam
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/ctl1/ctl1-R1.subsampled.80.merged.nodup.tagAlign.gz
Control 2
Filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/ctl2/ctl2-R1.subsampled.80.merged.nodup.bam
Raw BAM from alignergs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/ctl2/ctl2-R1.subsampled.80.merged.bam
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/ctl2/ctl2-R1.subsampled.80.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/pooled-ctl/ctl1-R1.subsampled.80.merged.nodup.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/pooled-rep/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/pooled-rep/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.pooled.tagAlign.gz
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep1/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep1/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep1/rep1-R1.subsampled.50.merged.nodup.bam
Raw BAM from alignergs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep1/rep1-R1.subsampled.50.merged.bam
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep1/rep1-R1.subsampled.50.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep2/pseudorep1/rep2-R1.subsampled.50.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep2/pseudorep2/rep2-R1.subsampled.50.merged.nodup.pr2.tagAlign.gz
Filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep2/rep2-R1.subsampled.50.merged.nodup.bam
Raw BAM from alignergs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep2/rep2-R1.subsampled.50.merged.bam
TAG-ALIGNgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/align/rep2/rep2-R1.subsampled.50.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.regionPeak.gz
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/peak/rep1/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.300K.regionPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peakgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/peak/rep2/pseudorep1/rep2-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep1/rep2-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep1/rep2-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep1/rep2-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep2/rep2-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep2/rep2-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep2/rep2-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/pseudorep2/rep2-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeakgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/peak/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl1/ctl1-R1.subsampled.80.merged.dup.qc
Library complexity QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl1/ctl1-R1.subsampled.80.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl1/ctl1-R1.subsampled.80.merged.samstats.qc
SAMstats log for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl1/ctl1-R1.subsampled.80.merged.nodup.samstats.qc
Control 2
Dup QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl2/ctl2-R1.subsampled.80.merged.dup.qc
Library complexity QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl2/ctl2-R1.subsampled.80.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl2/ctl2-R1.subsampled.80.merged.samstats.qc
SAMstats log for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/ctl2/ctl2-R1.subsampled.80.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in readsgs://encode-pipeline-test-samples/encode-chip-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-chip-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-chip-seq-pipeline/croo_example/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/qc/pooled-rep/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/pooled-rep/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.frip.qc
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in readsgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR loggs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-chip-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-chip-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-chip-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-chip-seq-pipeline/croo_example/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/qc/rep1/pseudorep1/rep1-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/pseudorep2/rep1-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plotgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation scoregs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.dup.qc
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.samstats.qc
SAMstats log for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1/rep1-R1.subsampled.50.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in readsgs://encode-pipeline-test-samples/encode-chip-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-chip-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-chip-seq-pipeline/croo_example/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plotgs://encode-pipeline-test-samples/encode-chip-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-chip-seq-pipeline/croo_example/qc/rep2/pseudorep1/rep2-R1.subsampled.50.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/pseudorep2/rep2-R1.subsampled.50.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plotgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation scoregs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.dup.qc
Fraction of peaks in readsgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.dupmark.lib_complexity.qc
SAMstats log for Raw BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.samstats.qc
SAMstats log for filtered BAMgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep2/rep2-R1.subsampled.50.merged.nodup.samstats.qc
Final HTML reportgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/qc.html
Final QC JSON filegs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/qc.json
Jensen-Shannon distance plotgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/rep1-R1.subsampled.50.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaksgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/pooled-rep/rep1-R1.subsampled.50.merged.nodup.pooled_x_ctl1-R1.subsampled.80.merged.nodup.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)gs://encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.pval.signal.bigwig
Task graph D cluster_pooled_rep Pooled replicate cluster_rep1 Replicate 1 cluster_rep2 Replicate 2 cluster_pooled_ctl Pooled control cluster_ctl1 Control 1 cluster_ctl2 Control 2 4344072593499672654 chip.macs2_signal_track_pooled 9111974781895016102 BW FC 4344072593499672654->9111974781895016102 -6496455822653794087 BW p-val 4344072593499672654->-6496455822653794087 -1630850447480584037 chip.call_peak_pooled -3114223235795776298 Peak (bfilt) -1630850447480584037->-3114223235795776298 3507479019311956121 Peak -1630850447480584037->3507479019311956121 150583477727836542 chip.idr_ppr 3507479019311956121->150583477727836542 -8314435775348587367 chip.idr 3507479019311956121->-8314435775348587367 -2732274808741061865 chip.overlap 3507479019311956121->-2732274808741061865 -3188769461718946175 chip.overlap_ppr 3507479019311956121->-3188769461718946175 -1470397919339165516 chip.pool_ta 5298590577444849882 TAG-ALIGN -1470397919339165516->5298590577444849882 5298590577444849882->4344072593499672654 5298590577444849882->-1630850447480584037 -3573875225006722077 chip.call_peak 5298590577444849882->-3573875225006722077 -7833595761068252034 chip.macs2_signal_track 5298590577444849882->-7833595761068252034 -1281479376654627962 chip.call_peak 5298590577444849882->-1281479376654627962 3537016993164398236 chip.macs2_signal_track 5298590577444849882->3537016993164398236 5298590577444849882->150583477727836542 5298590577444849882->-8314435775348587367 5298590577444849882->-2732274808741061865 -2158617377070646864 chip.reproducibility_overlap 5298590577444849882->-2158617377070646864 4348153068487806347 chip.reproducibility_idr 5298590577444849882->4348153068487806347 5298590577444849882->-3188769461718946175 7062500213295698442 Peak (bfilt) -3573875225006722077->7062500213295698442 792261851540241785 Peak -3573875225006722077->792261851540241785 792261851540241785->-8314435775348587367 792261851540241785->-2732274808741061865 792261851540241785->-2158617377070646864 792261851540241785->4348153068487806347 6403013148478317702 chip.bam2ta -7886578189134860566 TAG-ALIGN 6403013148478317702->-7886578189134860566 -7886578189134860566->-1470397919339165516 -7886578189134860566->-3573875225006722077 -7886578189134860566->-7833595761068252034 -7886578189134860566->-1281479376654627962 -7886578189134860566->3537016993164398236 -7886578189134860566->150583477727836542 -7886578189134860566->-2158617377070646864 -7886578189134860566->4348153068487806347 -7886578189134860566->-3188769461718946175 -7037008326450424134 chip.filter 8237190696955719871 SAMstats QC -7037008326450424134->8237190696955719871 847021509162465952 Filt/deduped BAM -7037008326450424134->847021509162465952 7981640907462567743 LibCmplx QC -7037008326450424134->7981640907462567743 847021509162465952->6403013148478317702 -8188485698551627545 chip.jsd 847021509162465952->-8188485698551627545 6682381387358299434 chip.align -8841534693057544213 SAMstats QC 6682381387358299434->-8841534693057544213 9126325593532033391 BAM 6682381387358299434->9126325593532033391 9126325593532033391->-7037008326450424134 928592811601117704 chip.xcor 3434639829380335587 XCOR Plot 928592811601117704->3434639829380335587 8281714592075326780 BW p-val -7833595761068252034->8281714592075326780 -8395415883789264546 BW FC -7833595761068252034->-8395415883789264546 3270133193679878418 FASTQ R1 (1) 3270133193679878418->6682381387358299434 3270133193679878418->928592811601117704 -7159132272311431266 FASTQ R2 (1) -7159132272311431266->6682381387358299434 -7159132272311431266->928592811601117704 -6462544239903484589 Peak (bfilt) -1281479376654627962->-6462544239903484589 -5330154166555029605 Peak -1281479376654627962->-5330154166555029605 -5330154166555029605->-8314435775348587367 -5330154166555029605->-2732274808741061865 -5330154166555029605->-2158617377070646864 -5330154166555029605->4348153068487806347 4901504885052826357 chip.bam2ta 7862740099324830876 TAG-ALIGN 4901504885052826357->7862740099324830876 7862740099324830876->-1470397919339165516 7862740099324830876->-3573875225006722077 7862740099324830876->-7833595761068252034 7862740099324830876->-1281479376654627962 7862740099324830876->3537016993164398236 7862740099324830876->150583477727836542 7862740099324830876->-2158617377070646864 7862740099324830876->4348153068487806347 7862740099324830876->-3188769461718946175 7352270273089498392 chip.filter 2767496884623073578 SAMstats QC 7352270273089498392->2767496884623073578 8778381448708961658 Filt/deduped BAM 7352270273089498392->8778381448708961658 -3446346223224817224 LibCmplx QC 7352270273089498392->-3446346223224817224 8778381448708961658->4901504885052826357 8778381448708961658->-8188485698551627545 5018450783936928917 chip.align -126028945660998534 SAMstats QC 5018450783936928917->-126028945660998534 -8304141177492365428 BAM 5018450783936928917->-8304141177492365428 -8304141177492365428->7352270273089498392 268876639578837298 chip.xcor -2595624938461636596 XCOR Plot 268876639578837298->-2595624938461636596 6819556894314071561 BW FC 3537016993164398236->6819556894314071561 -8875679107050825578 BW p-val 3537016993164398236->-8875679107050825578 4621613172618897093 FASTQ R1 (1) 4621613172618897093->5018450783936928917 4621613172618897093->268876639578837298 -5255048111075531952 FASTQ R2 (1) -5255048111075531952->5018450783936928917 -5255048111075531952->268876639578837298 -7933308242392080421 chip.pool_ta_ctl -2898525053967968519 TAG-ALIGN -7933308242392080421->-2898525053967968519 -2898525053967968519->4344072593499672654 -2898525053967968519->-1630850447480584037 -2898525053967968519->-3573875225006722077 -2898525053967968519->-7833595761068252034 -2898525053967968519->-1281479376654627962 -2898525053967968519->3537016993164398236 -2898525053967968519->150583477727836542 -2898525053967968519->-2158617377070646864 -2898525053967968519->4348153068487806347 -2898525053967968519->-3188769461718946175 -3984259744349884025 chip.bam2ta_ctl 84173761766599462 TAG-ALIGN -3984259744349884025->84173761766599462 84173761766599462->-3573875225006722077 84173761766599462->-7833595761068252034 84173761766599462->-1281479376654627962 84173761766599462->3537016993164398236 84173761766599462->-7933308242392080421 84173761766599462->-2158617377070646864 84173761766599462->4348153068487806347 -1452730126385579783 chip.filter_ctl -4940115654033938144 SAMstats QC -1452730126385579783->-4940115654033938144 6819195099930775699 Filt/deduped BAM -1452730126385579783->6819195099930775699 307546130393178340 LibCmplx QC -1452730126385579783->307546130393178340 6819195099930775699->-3984259744349884025 6819195099930775699->-8188485698551627545 7729602345818650310 chip.align_ctl -7804096280209802068 BAM 7729602345818650310->-7804096280209802068 -6839596464364955512 SAMstats QC 7729602345818650310->-6839596464364955512 -7804096280209802068->-1452730126385579783 4946053171603178510 FASTQ R1 (1) 4946053171603178510->7729602345818650310 516903364674754624 FASTQ R2 (1) 516903364674754624->7729602345818650310 -3841489018610518059 chip.bam2ta_ctl -375701903574196676 TAG-ALIGN -3841489018610518059->-375701903574196676 -375701903574196676->-3573875225006722077 -375701903574196676->-7833595761068252034 -375701903574196676->-1281479376654627962 -375701903574196676->3537016993164398236 -375701903574196676->-7933308242392080421 -375701903574196676->-2158617377070646864 -375701903574196676->4348153068487806347 6437723113511693324 chip.filter_ctl -6742098959227817550 SAMstats QC 6437723113511693324->-6742098959227817550 5951416549808066028 Filt/deduped BAM 6437723113511693324->5951416549808066028 -2890018019672358971 LibCmplx QC 6437723113511693324->-2890018019672358971 5951416549808066028->-3841489018610518059 5951416549808066028->-8188485698551627545 7792253134001593615 chip.align_ctl 2261234721367120232 BAM 7792253134001593615->2261234721367120232 3488322329371940077 SAMstats QC 7792253134001593615->3488322329371940077 2261234721367120232->6437723113511693324 -3482109367850779780 FASTQ R1 (1) -3482109367850779780->7792253134001593615 -7791741650662750089 FASTQ R2 (1) -7791741650662750089->7792253134001593615 -3683187070114905896 IDR Plot ppr 150583477727836542->-3683187070114905896 -4342606802045237711 IDR Peak ppr 150583477727836542->-4342606802045237711 -4342606802045237711->4348153068487806347 8335102902854687868 IDR Plot rep1_vs_rep2 -8314435775348587367->8335102902854687868 4004184287001424464 IDR NPeak rep1_vs_rep2 -8314435775348587367->4004184287001424464 4004184287001424464->4348153068487806347 4533580746475544099 Overlap Peak rep1_vs_rep2 -2732274808741061865->4533580746475544099 4533580746475544099->-2158617377070646864 4892444487004014348 Overlap Peak optimal -2158617377070646864->4892444487004014348 6128854125583512709 Overlap reproducibility -2158617377070646864->6128854125583512709 253989869128204313 IDR Peak optimal 4348153068487806347->253989869128204313 8682409414388000205 IDR reproducibility 4348153068487806347->8682409414388000205 -4179663757503693158 Overlap Peak ppr -3188769461718946175->-4179663757503693158 -4179663757503693158->-2158617377070646864 548475180015330734 JSD Plot -8188485698551627545->548475180015330734

UCSC browser tracks

UCSC track hub plain text
track type=bigWig name="MACS2 p-val (rep1)" priority=1 smoothingWindow=off maxHeightPixels=80:60:40 color=255,0,0 autoScale=off viewLimits=0:40 visibility=full bigDataUrl="http://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/rep1/rep1-R1.subsampled.50.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig"
track type=bigWig name="MACS2 p-val (rep2)" priority=2 smoothingWindow=off maxHeightPixels=80:60:40 color=255,0,0 autoScale=off viewLimits=0:40 visibility=full bigDataUrl="http://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/croo_example/signal/rep2/rep2-R1.subsampled.50.merged.nodup_x_ctl_for_rep2.pval.signal.bigwig"
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