File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/ctl1/ENCFF000VWD.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/ctl1/ENCFF000VWD.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/ctl1/ENCFF000VWD.merged.nodup.tagAlign.gz
Control 2
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/ctl2/ENCFF000VWK.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/ctl2/ENCFF000VWK.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/ctl2/ENCFF000VWK.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/pooled-ctl/basename_prefix.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep1/pseudorep1/ENCFF000WGD.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep1/pseudorep2/ENCFF000WGD.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep1/ENCFF000WGD.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep1/ENCFF000WGD.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep1/ENCFF000WGD.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep2/pseudorep1/ENCFF000WGE.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep2/pseudorep2/ENCFF000WGE.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep2/ENCFF000WGE.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep2/ENCFF000WGE.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000EAA/align/rep2/ENCFF000WGE.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.gz
Pooled replicate
Pseudoreplicate 1
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Rep1 vs. rep2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.gz
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep1/ENCFF000WGD.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep1/ENCFF000WGD.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep1/ENCFF000WGD.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep1/ENCFF000WGD.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep2/ENCFF000WGD.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep2/ENCFF000WGD.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep2/ENCFF000WGD.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/pseudorep2/ENCFF000WGD.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.300K.regionPeak.gz
Replicate 2
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep1/ENCFF000WGE.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep1/ENCFF000WGE.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep1/ENCFF000WGE.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep1/ENCFF000WGE.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep2/ENCFF000WGE.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep2/ENCFF000WGE.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep2/ENCFF000WGE.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/pseudorep2/ENCFF000WGE.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/ENCFF000WGE.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/ENCFF000WGE.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/ENCFF000WGE.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000EAA/peak/rep2/ENCFF000WGE.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl1/ENCFF000VWD.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl1/ENCFF000VWD.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl1/ENCFF000VWD.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl1/ENCFF000VWD.merged.nodup.samstats.qc
Control 2
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl2/ENCFF000VWK.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl2/ENCFF000VWK.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl2/ENCFF000VWK.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ctl2/ENCFF000VWK.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.unthresholded-peaks.txt.png
Pooled replicate
Pseudoreplicate 1
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.frip.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.frip.qc
Rep1 vs. vs vs. rep2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.png
Replicate 1
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/pseudorep1/ENCFF000WGD.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/pseudorep2/ENCFF000WGD.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep1/ENCFF000WGD.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/pseudorep1/ENCFF000WGE.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/pseudorep2/ENCFF000WGE.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/rep2/ENCFF000WGE.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/ENCFF000WGD.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000EAA/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EAA/signal/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EAA/signal/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.pval.signal.bigwig
Replicate 1
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EAA/signal/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EAA/signal/rep1/ENCFF000WGD.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000EAA/signal/rep2/ENCFF000WGE.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000EAA/signal/rep2/ENCFF000WGE.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 -4635007970691421827 chip.macs2_signal_track_pooled 2420283234339746117 BW FC -4635007970691421827->2420283234339746117 2766468700153560881 BW p-val -4635007970691421827->2766468700153560881 9039746168392528887 chip.call_peak_pooled 5681959308697567595 Peak (bfilt) 9039746168392528887->5681959308697567595 -4093347753034280453 Peak 9039746168392528887->-4093347753034280453 -2388343313807855889 chip.idr_ppr -4093347753034280453->-2388343313807855889 750665349348263613 chip.idr -4093347753034280453->750665349348263613 4206660417262610027 chip.overlap -4093347753034280453->4206660417262610027 161460094975018432 chip.overlap_ppr -4093347753034280453->161460094975018432 7381777647747935241 chip.pool_ta -8975301951283467262 TAG-ALIGN 7381777647747935241->-8975301951283467262 -8975301951283467262->-4635007970691421827 -8975301951283467262->9039746168392528887 -8140332563797197063 chip.call_peak -8975301951283467262->-8140332563797197063 2549230103445879801 chip.macs2_signal_track -8975301951283467262->2549230103445879801 8372440977851715476 chip.call_peak -8975301951283467262->8372440977851715476 -1049234159640230774 chip.macs2_signal_track -8975301951283467262->-1049234159640230774 -8975301951283467262->-2388343313807855889 -8975301951283467262->750665349348263613 -8975301951283467262->4206660417262610027 2955176430769886697 chip.reproducibility_overlap -8975301951283467262->2955176430769886697 -3749651622864499112 chip.reproducibility_idr -8975301951283467262->-3749651622864499112 -8975301951283467262->161460094975018432 -3491019297218508234 Peak (bfilt) -8140332563797197063->-3491019297218508234 1216662049410602453 Peak -8140332563797197063->1216662049410602453 1216662049410602453->750665349348263613 1216662049410602453->4206660417262610027 1216662049410602453->2955176430769886697 1216662049410602453->-3749651622864499112 311826507134230306 chip.bam2ta 8255556942696432055 TAG-ALIGN 311826507134230306->8255556942696432055 8255556942696432055->7381777647747935241 8255556942696432055->-8140332563797197063 8255556942696432055->2549230103445879801 8255556942696432055->8372440977851715476 8255556942696432055->-1049234159640230774 8255556942696432055->-2388343313807855889 8255556942696432055->2955176430769886697 8255556942696432055->-3749651622864499112 8255556942696432055->161460094975018432 3870226351278966537 chip.filter 1928674615268943565 SAMstats QC 3870226351278966537->1928674615268943565 7458921953635434505 Filt/deduped BAM 3870226351278966537->7458921953635434505 6855489097731415453 LibCmplx QC 3870226351278966537->6855489097731415453 7458921953635434505->311826507134230306 8797624716522969246 chip.jsd 7458921953635434505->8797624716522969246 -2005000756424525619 chip.align -7643834813016189946 BAM -2005000756424525619->-7643834813016189946 276180015188517811 SAMstats QC -2005000756424525619->276180015188517811 -7643834813016189946->3870226351278966537 2376544795840129890 chip.xcor 6021587887868560637 XCOR Plot 2376544795840129890->6021587887868560637 7895403487505584024 BW FC 2549230103445879801->7895403487505584024 -141790162602638216 BW p-val 2549230103445879801->-141790162602638216 3667155568962378155 FASTQ R1 (1) 3667155568962378155->-2005000756424525619 3667155568962378155->2376544795840129890 76776448438582583 Peak (bfilt) 8372440977851715476->76776448438582583 -8828086548203758431 Peak 8372440977851715476->-8828086548203758431 -8828086548203758431->750665349348263613 -8828086548203758431->4206660417262610027 -8828086548203758431->2955176430769886697 -8828086548203758431->-3749651622864499112 -3509270056495367931 chip.bam2ta 6487477517819176872 TAG-ALIGN -3509270056495367931->6487477517819176872 6487477517819176872->7381777647747935241 6487477517819176872->-8140332563797197063 6487477517819176872->2549230103445879801 6487477517819176872->8372440977851715476 6487477517819176872->-1049234159640230774 6487477517819176872->-2388343313807855889 6487477517819176872->2955176430769886697 6487477517819176872->-3749651622864499112 6487477517819176872->161460094975018432 -5966772976978077431 chip.filter 4493171645049743358 SAMstats QC -5966772976978077431->4493171645049743358 352291307580364636 Filt/deduped BAM -5966772976978077431->352291307580364636 2644617507249854690 LibCmplx QC -5966772976978077431->2644617507249854690 352291307580364636->-3509270056495367931 352291307580364636->8797624716522969246 -9188601707897562872 chip.align -6911801443818158014 SAMstats QC -9188601707897562872->-6911801443818158014 6415836396543704800 BAM -9188601707897562872->6415836396543704800 6415836396543704800->-5966772976978077431 -8898256796145151887 chip.xcor -3375714799505791776 XCOR Plot -8898256796145151887->-3375714799505791776 -4868899195568390725 BW FC -1049234159640230774->-4868899195568390725 3133583835355623175 BW p-val -1049234159640230774->3133583835355623175 -2802184258455024886 FASTQ R1 (1) -2802184258455024886->-9188601707897562872 -2802184258455024886->-8898256796145151887 996443708732630025 chip.pool_ta_ctl -7984216493855583717 TAG-ALIGN 996443708732630025->-7984216493855583717 -7984216493855583717->-4635007970691421827 -7984216493855583717->9039746168392528887 -7984216493855583717->-8140332563797197063 -7984216493855583717->2549230103445879801 -7984216493855583717->8372440977851715476 -7984216493855583717->-1049234159640230774 -7984216493855583717->-2388343313807855889 -7984216493855583717->2955176430769886697 -7984216493855583717->-3749651622864499112 -7984216493855583717->161460094975018432 -2431575790493720999 chip.bam2ta_ctl -989195365767343265 TAG-ALIGN -2431575790493720999->-989195365767343265 -989195365767343265->-8140332563797197063 -989195365767343265->2549230103445879801 -989195365767343265->8372440977851715476 -989195365767343265->-1049234159640230774 -989195365767343265->996443708732630025 -989195365767343265->2955176430769886697 -989195365767343265->-3749651622864499112 -1846792763913506307 chip.filter_ctl -4881714100699231667 SAMstats QC -1846792763913506307->-4881714100699231667 4467549140508684867 Filt/deduped BAM -1846792763913506307->4467549140508684867 1627082833967817059 LibCmplx QC -1846792763913506307->1627082833967817059 4467549140508684867->-2431575790493720999 4467549140508684867->8797624716522969246 5621110771871177097 chip.align_ctl -54982771966114402 SAMstats QC 5621110771871177097->-54982771966114402 -3530067385151768411 BAM 5621110771871177097->-3530067385151768411 -3530067385151768411->-1846792763913506307 -3094042426002805990 FASTQ R1 (1) -3094042426002805990->5621110771871177097 -1886116730056271107 chip.bam2ta_ctl 6885359527848306237 TAG-ALIGN -1886116730056271107->6885359527848306237 6885359527848306237->-8140332563797197063 6885359527848306237->2549230103445879801 6885359527848306237->8372440977851715476 6885359527848306237->-1049234159640230774 6885359527848306237->996443708732630025 6885359527848306237->2955176430769886697 6885359527848306237->-3749651622864499112 -5724894015405948944 chip.filter_ctl 2262982720137670645 SAMstats QC -5724894015405948944->2262982720137670645 -6159044426107347918 Filt/deduped BAM -5724894015405948944->-6159044426107347918 7212172661984113972 LibCmplx QC -5724894015405948944->7212172661984113972 -6159044426107347918->-1886116730056271107 -6159044426107347918->8797624716522969246 -4510086248072607932 chip.align_ctl 8814707997198512820 SAMstats QC -4510086248072607932->8814707997198512820 -2228566437994143915 BAM -4510086248072607932->-2228566437994143915 -2228566437994143915->-5724894015405948944 4932319796420394898 FASTQ R1 (1) 4932319796420394898->-4510086248072607932 4864790658020480324 IDR Plot ppr -2388343313807855889->4864790658020480324 1946057682338185914 IDR Peak ppr -2388343313807855889->1946057682338185914 1946057682338185914->-3749651622864499112 8998955780563126521 IDR Plot rep1_vs_rep2 750665349348263613->8998955780563126521 3709428008658594005 IDR NPeak rep1_vs_rep2 750665349348263613->3709428008658594005 3709428008658594005->-3749651622864499112 2453031914792337701 Overlap Peak rep1_vs_rep2 4206660417262610027->2453031914792337701 2453031914792337701->2955176430769886697 7756079859165320896 Overlap Peak optimal 2955176430769886697->7756079859165320896 2458184463102119868 Overlap reproducibility 2955176430769886697->2458184463102119868 -4146214600150908851 IDR Peak optimal -3749651622864499112->-4146214600150908851 -4660625257576287906 IDR reproducibility -3749651622864499112->-4660625257576287906 8737836911011098428 Overlap Peak ppr 161460094975018432->8737836911011098428 8737836911011098428->2955176430769886697 5786738349536690910 JSD Plot 8797624716522969246->5786738349536690910

UCSC browser tracks

UCSC track hub plain text 
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UCSC track hub encoded URL (Use this for browser's parameter &hgct_customText=) 
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