File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/ctl1/ENCFF000VWD.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/ctl1/ENCFF000VWD.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/ctl1/ENCFF000VWD.merged.nodup.tagAlign.gz
Control 2
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/ctl2/ENCFF000VWK.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/ctl2/ENCFF000VWK.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/ctl2/ENCFF000VWK.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/pooled-ctl/basename_prefix.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep1/pseudorep1/ENCFF000VUJ.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep1/pseudorep2/ENCFF000VUJ.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep1/ENCFF000VUJ.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep1/ENCFF000VUJ.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep1/ENCFF000VUJ.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep2/pseudorep1/ENCFF000VUL.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep2/pseudorep2/ENCFF000VUL.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep2/ENCFF000VUL.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep2/ENCFF000VUL.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR000DYY/align/rep2/ENCFF000VUL.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/peak/rep1/pseudorep1/ENCFF000VUJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep1/ENCFF000VUJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep1/ENCFF000VUJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep1/ENCFF000VUJ.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep2/ENCFF000VUJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep2/ENCFF000VUJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep2/ENCFF000VUJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/pseudorep2/ENCFF000VUJ.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/ENCFF000VUJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/ENCFF000VUJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/ENCFF000VUJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep1/ENCFF000VUJ.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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/peak/rep2/pseudorep1/ENCFF000VUL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep1/ENCFF000VUL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep1/ENCFF000VUL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep1/ENCFF000VUL.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep2/ENCFF000VUL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep2/ENCFF000VUL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep2/ENCFF000VUL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/pseudorep2/ENCFF000VUL.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/ENCFF000VUL.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/ENCFF000VUL.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/ENCFF000VUL.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR000DYY/peak/rep2/ENCFF000VUL.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl1/ENCFF000VWD.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl1/ENCFF000VWD.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl1/ENCFF000VWD.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl1/ENCFF000VWD.merged.nodup.samstats.qc
Control 2
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl2/ENCFF000VWK.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl2/ENCFF000VWK.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl2/ENCFF000VWK.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ctl2/ENCFF000VWK.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/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/ENCSR000DYY/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/qc/rep1/pseudorep1/ENCFF000VUJ.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/pseudorep2/ENCFF000VUJ.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep1/ENCFF000VUJ.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/qc/rep2/pseudorep1/ENCFF000VUL.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/pseudorep2/ENCFF000VUL.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/rep2/ENCFF000VUL.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/ENCFF000VUJ.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR000DYY/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000DYY/signal/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000DYY/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/ENCSR000DYY/signal/rep1/ENCFF000VUJ.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000DYY/signal/rep1/ENCFF000VUJ.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR000DYY/signal/rep2/ENCFF000VUL.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR000DYY/signal/rep2/ENCFF000VUL.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 2538329015686417292 chip.macs2_signal_track_pooled -1816703051829787735 BW p-val 2538329015686417292->-1816703051829787735 2775746463943198248 BW FC 2538329015686417292->2775746463943198248 4650438821738454526 chip.call_peak_pooled 8809663891187939726 Peak (bfilt) 4650438821738454526->8809663891187939726 -6889151252366897966 Peak 4650438821738454526->-6889151252366897966 -2068899413716740298 chip.idr_ppr -6889151252366897966->-2068899413716740298 2846523377404331261 chip.idr -6889151252366897966->2846523377404331261 -2175918447051848066 chip.overlap -6889151252366897966->-2175918447051848066 -2256529149971478203 chip.overlap_ppr -6889151252366897966->-2256529149971478203 7696799157783431679 chip.pool_ta -480296251682281214 TAG-ALIGN 7696799157783431679->-480296251682281214 -480296251682281214->2538329015686417292 -480296251682281214->4650438821738454526 -8528829578200752629 chip.call_peak -480296251682281214->-8528829578200752629 7865816947189606709 chip.macs2_signal_track -480296251682281214->7865816947189606709 -1749578958629299969 chip.call_peak -480296251682281214->-1749578958629299969 -2625899830136561917 chip.macs2_signal_track -480296251682281214->-2625899830136561917 -480296251682281214->-2068899413716740298 -480296251682281214->2846523377404331261 -480296251682281214->-2175918447051848066 -8334814039535237228 chip.reproducibility_overlap -480296251682281214->-8334814039535237228 8261557255894418360 chip.reproducibility_idr -480296251682281214->8261557255894418360 -480296251682281214->-2256529149971478203 3853517163323679972 Peak (bfilt) -8528829578200752629->3853517163323679972 -8635920118613041938 Peak -8528829578200752629->-8635920118613041938 -8635920118613041938->2846523377404331261 -8635920118613041938->-2175918447051848066 -8635920118613041938->-8334814039535237228 -8635920118613041938->8261557255894418360 -2311897742157000185 chip.bam2ta -960741270378636955 TAG-ALIGN -2311897742157000185->-960741270378636955 -960741270378636955->7696799157783431679 -960741270378636955->-8528829578200752629 -960741270378636955->7865816947189606709 -960741270378636955->-1749578958629299969 -960741270378636955->-2625899830136561917 -960741270378636955->-2068899413716740298 -960741270378636955->-8334814039535237228 -960741270378636955->8261557255894418360 -960741270378636955->-2256529149971478203 795669837257634333 chip.filter -1259841239183729083 SAMstats QC 795669837257634333->-1259841239183729083 3044461321890566546 Filt/deduped BAM 795669837257634333->3044461321890566546 -6024937237247651372 LibCmplx QC 795669837257634333->-6024937237247651372 3044461321890566546->-2311897742157000185 2287998539214592680 chip.jsd 3044461321890566546->2287998539214592680 8283051373431059090 chip.align 3521094389872664490 SAMstats QC 8283051373431059090->3521094389872664490 7643088646557957418 BAM 8283051373431059090->7643088646557957418 7643088646557957418->795669837257634333 -4108999308660663548 chip.xcor -684091764657169361 XCOR Plot -4108999308660663548->-684091764657169361 -5091308861706960796 BW p-val 7865816947189606709->-5091308861706960796 -2851072774923674440 BW FC 7865816947189606709->-2851072774923674440 -6209446799404741146 FASTQ R1 (1) -6209446799404741146->8283051373431059090 -6209446799404741146->-4108999308660663548 5323881296928218344 Peak (bfilt) -1749578958629299969->5323881296928218344 -8357174715535008020 Peak -1749578958629299969->-8357174715535008020 -8357174715535008020->2846523377404331261 -8357174715535008020->-2175918447051848066 -8357174715535008020->-8334814039535237228 -8357174715535008020->8261557255894418360 -7757692303811803879 chip.bam2ta -3184171109712387534 TAG-ALIGN -7757692303811803879->-3184171109712387534 -3184171109712387534->7696799157783431679 -3184171109712387534->-8528829578200752629 -3184171109712387534->7865816947189606709 -3184171109712387534->-1749578958629299969 -3184171109712387534->-2625899830136561917 -3184171109712387534->-2068899413716740298 -3184171109712387534->-8334814039535237228 -3184171109712387534->8261557255894418360 -3184171109712387534->-2256529149971478203 8087444963853448803 chip.filter 6639574079328510286 SAMstats QC 8087444963853448803->6639574079328510286 9048411715146369542 Filt/deduped BAM 8087444963853448803->9048411715146369542 4562997555839262401 LibCmplx QC 8087444963853448803->4562997555839262401 9048411715146369542->-7757692303811803879 9048411715146369542->2287998539214592680 -2613128969054028005 chip.align 4496294187056232035 SAMstats QC -2613128969054028005->4496294187056232035 -7978601311569426935 BAM -2613128969054028005->-7978601311569426935 -7978601311569426935->8087444963853448803 2679226749585895384 chip.xcor 5830655667339898755 XCOR Plot 2679226749585895384->5830655667339898755 2418759401649271565 BW p-val -2625899830136561917->2418759401649271565 6453724988822109643 BW FC -2625899830136561917->6453724988822109643 5392565105028248285 FASTQ R1 (1) 5392565105028248285->-2613128969054028005 5392565105028248285->2679226749585895384 3991043456044716372 chip.pool_ta_ctl 1549663103906284483 TAG-ALIGN 3991043456044716372->1549663103906284483 1549663103906284483->2538329015686417292 1549663103906284483->4650438821738454526 1549663103906284483->-8528829578200752629 1549663103906284483->7865816947189606709 1549663103906284483->-1749578958629299969 1549663103906284483->-2625899830136561917 1549663103906284483->-2068899413716740298 1549663103906284483->-8334814039535237228 1549663103906284483->8261557255894418360 1549663103906284483->-2256529149971478203 -8149460701783935830 chip.bam2ta_ctl 306297257149567500 TAG-ALIGN -8149460701783935830->306297257149567500 306297257149567500->-8528829578200752629 306297257149567500->7865816947189606709 306297257149567500->-1749578958629299969 306297257149567500->-2625899830136561917 306297257149567500->3991043456044716372 306297257149567500->-8334814039535237228 306297257149567500->8261557255894418360 -3216788135659530501 chip.filter_ctl -8751451658909137710 SAMstats QC -3216788135659530501->-8751451658909137710 -7006974968996961375 Filt/deduped BAM -3216788135659530501->-7006974968996961375 6974952539498549414 LibCmplx QC -3216788135659530501->6974952539498549414 -7006974968996961375->-8149460701783935830 -7006974968996961375->2287998539214592680 -5522121638924555239 chip.align_ctl -6550929951981597773 SAMstats QC -5522121638924555239->-6550929951981597773 4535776046287004188 BAM -5522121638924555239->4535776046287004188 4535776046287004188->-3216788135659530501 -8339370841179518929 FASTQ R1 (1) -8339370841179518929->-5522121638924555239 1859528257412954336 chip.bam2ta_ctl 4157128958310824755 TAG-ALIGN 1859528257412954336->4157128958310824755 4157128958310824755->-8528829578200752629 4157128958310824755->7865816947189606709 4157128958310824755->-1749578958629299969 4157128958310824755->-2625899830136561917 4157128958310824755->3991043456044716372 4157128958310824755->-8334814039535237228 4157128958310824755->8261557255894418360 9113085076368393409 chip.filter_ctl 2204090640491042909 SAMstats QC 9113085076368393409->2204090640491042909 -7969751014355738659 Filt/deduped BAM 9113085076368393409->-7969751014355738659 1188095057615174451 LibCmplx QC 9113085076368393409->1188095057615174451 -7969751014355738659->1859528257412954336 -7969751014355738659->2287998539214592680 850645663477653695 chip.align_ctl 6303315157698997701 SAMstats QC 850645663477653695->6303315157698997701 8507037058819923296 BAM 850645663477653695->8507037058819923296 8507037058819923296->9113085076368393409 6614855333358286038 FASTQ R1 (1) 6614855333358286038->850645663477653695 7527340591887093650 IDR Plot ppr -2068899413716740298->7527340591887093650 -5930436817580565642 IDR Peak ppr -2068899413716740298->-5930436817580565642 -5930436817580565642->8261557255894418360 -4748990283338453094 IDR Plot rep1_vs_rep2 2846523377404331261->-4748990283338453094 8184322138420343974 IDR NPeak rep1_vs_rep2 2846523377404331261->8184322138420343974 8184322138420343974->8261557255894418360 -3258234118465768380 Overlap Peak rep1_vs_rep2 -2175918447051848066->-3258234118465768380 -3258234118465768380->-8334814039535237228 1800800857938920832 Overlap Peak optimal -8334814039535237228->1800800857938920832 -2164717389926539558 Overlap reproducibility -8334814039535237228->-2164717389926539558 5570775371102248099 IDR Peak optimal 8261557255894418360->5570775371102248099 -8229200682129761128 IDR reproducibility 8261557255894418360->-8229200682129761128 -1853790345036920540 Overlap Peak ppr -2256529149971478203->-1853790345036920540 -1853790345036920540->-8334814039535237228 1533180180229292907 JSD Plot 2287998539214592680->1533180180229292907

UCSC browser tracks

UCSC track hub plain text 
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