File table
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FilesPath
Alignment
Control 1
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/ctl1/ENCFF002ECW.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/ctl1/ENCFF002ECW.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/ctl1/ENCFF002ECW.merged.nodup.tagAlign.gz
Control 2
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/ctl2/ENCFF002ECS.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/ctl2/ENCFF002ECS.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/ctl2/ENCFF002ECS.merged.nodup.tagAlign.gz
Pooled control
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/pooled-ctl/basename_prefix.pooled.tagAlign.gz
Pooled replicate
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/pooled-rep/basename_prefix.pooled.tagAlign.gz
Replicate 1
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep1/pseudorep1/ENCFF002EWO.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep1/pseudorep2/ENCFF002EWO.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep1/ENCFF002EWO.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep1/ENCFF002EWO.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep1/ENCFF002EWO.merged.nodup.tagAlign.gz
Replicate 2
Pseudoreplicate 1
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep2/pseudorep1/ENCFF002EWP.merged.nodup.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep2/pseudorep2/ENCFF002EWP.merged.nodup.pr2.tagAlign.gz
Filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep2/ENCFF002EWP.merged.nodup.bam
Raw BAM from aligner/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep2/ENCFF002EWP.merged.bam
TAG-ALIGN/srv/www/kundaje/natprot_chip/ENCSR412CTM/align/rep2/ENCFF002EWP.merged.nodup.tagAlign.gz
Peak
IDR reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz
Overlap reproducibility
Conservative peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz
Conservative peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb
Conservative peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz
Optimal peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz
Optimal peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb
Optimal peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz
Pooled pseudoreplicate 1 vs. 2
Blacklist-filtered IDR peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz
Blacklist-filtered IDR peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb
Blacklist-filtered IDR peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz
Blacklist-filtered overlap peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/peak/rep1/pseudorep1/ENCFF002EWO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep1/ENCFF002EWO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep1/ENCFF002EWO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep1/ENCFF002EWO.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep2/ENCFF002EWO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep2/ENCFF002EWO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep2/ENCFF002EWO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/pseudorep2/ENCFF002EWO.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/ENCFF002EWO.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/ENCFF002EWO.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/ENCFF002EWO.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep1/ENCFF002EWO.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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz
Blacklist-filtered overlap peak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb
Blacklist-filtered overlap peak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz
Unthresholded raw IDR peak/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/peak/rep2/pseudorep1/ENCFF002EWP.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep1/ENCFF002EWP.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep1/ENCFF002EWP.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep1/ENCFF002EWP.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep2/ENCFF002EWP.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep2/ENCFF002EWP.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep2/ENCFF002EWP.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/pseudorep2/ENCFF002EWP.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz
Blacklist-filtered narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/ENCFF002EWP.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz
Blacklist-filtered narrowpeak (BigBed)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/ENCFF002EWP.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb
Blacklist-filtered narrowpeak (hammock)/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/ENCFF002EWP.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz
Raw narrowpeak/srv/www/kundaje/natprot_chip/ENCSR412CTM/peak/rep2/ENCFF002EWP.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz
QC and logs
Control 1
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl1/ENCFF002ECW.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl1/ENCFF002ECW.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl1/ENCFF002ECW.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl1/ENCFF002ECW.merged.nodup.samstats.qc
Control 2
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl2/ENCFF002ECS.merged.dup.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl2/ENCFF002ECS.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl2/ENCFF002ECS.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ctl2/ENCFF002ECS.merged.nodup.samstats.qc
Pooled pseudoreplicate 1 vs. 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/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/ENCSR412CTM/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/qc/rep1/pseudorep1/ENCFF002EWO.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/pseudorep2/ENCFF002EWO.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep1/ENCFF002EWO.merged.nodup.samstats.qc
Replicate 2
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc
IDR log/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log
IDR plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/qc/rep2/pseudorep1/ENCFF002EWP.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/pseudorep2/ENCFF002EWP.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc
Cross-correlation Plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png
Cross-correlation score/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.trim_50bp.filt.no_chrM.15M.cc.qc
Dup QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.dup.qc
Fraction of peaks in reads/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc
Library complexity QC for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.lib_complexity.qc
SAMstats log for Raw BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.samstats.qc
SAMstats log for filtered BAM/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/rep2/ENCFF002EWP.merged.nodup.samstats.qc
Final HTML report/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/qc.html
Final QC JSON file/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/qc.json
Jensen-Shannon distance plot/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/ENCFF002EWO.merged.nodup.jsd_plot.png
Reproducibility QC for IDR peaks/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaks/srv/www/kundaje/natprot_chip/ENCSR412CTM/qc/idr.reproducibility.qc
Signal
Pooled replicate
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR412CTM/signal/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR412CTM/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/ENCSR412CTM/signal/rep1/ENCFF002EWO.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR412CTM/signal/rep1/ENCFF002EWO.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig
Replicate 2
MACS2 signal track (fold-enrichment)/srv/www/kundaje/natprot_chip/ENCSR412CTM/signal/rep2/ENCFF002EWP.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig
MACS2 signal track (p-val)/srv/www/kundaje/natprot_chip/ENCSR412CTM/signal/rep2/ENCFF002EWP.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 2382572364002699489 chip.macs2_signal_track_pooled 9184558359560302830 BW p-val 2382572364002699489->9184558359560302830 -7425956193502132896 BW FC 2382572364002699489->-7425956193502132896 -4365252832810290087 chip.call_peak_pooled 6863685402504850710 Peak (bfilt) -4365252832810290087->6863685402504850710 403936698625108776 Peak -4365252832810290087->403936698625108776 5590104336072004446 chip.idr_ppr 403936698625108776->5590104336072004446 -8489622891355707258 chip.idr 403936698625108776->-8489622891355707258 4551850613035248723 chip.overlap 403936698625108776->4551850613035248723 -1248208489229323032 chip.overlap_ppr 403936698625108776->-1248208489229323032 6866839613220246045 chip.pool_ta 1141118653182770455 TAG-ALIGN 6866839613220246045->1141118653182770455 1141118653182770455->2382572364002699489 1141118653182770455->-4365252832810290087 4365031997116084313 chip.call_peak 1141118653182770455->4365031997116084313 -5685839581835457289 chip.macs2_signal_track 1141118653182770455->-5685839581835457289 -8893451595391182000 chip.call_peak 1141118653182770455->-8893451595391182000 -9010107788625766273 chip.macs2_signal_track 1141118653182770455->-9010107788625766273 1141118653182770455->5590104336072004446 1141118653182770455->-8489622891355707258 1141118653182770455->4551850613035248723 -8679020406282899939 chip.reproducibility_overlap 1141118653182770455->-8679020406282899939 4237408165698940119 chip.reproducibility_idr 1141118653182770455->4237408165698940119 1141118653182770455->-1248208489229323032 -3000871110125136300 Peak (bfilt) 4365031997116084313->-3000871110125136300 -4450597132961724839 Peak 4365031997116084313->-4450597132961724839 -4450597132961724839->-8489622891355707258 -4450597132961724839->4551850613035248723 -4450597132961724839->-8679020406282899939 -4450597132961724839->4237408165698940119 3241724654863557108 chip.bam2ta 2872791921243764015 TAG-ALIGN 3241724654863557108->2872791921243764015 2872791921243764015->6866839613220246045 2872791921243764015->4365031997116084313 2872791921243764015->-5685839581835457289 2872791921243764015->-8893451595391182000 2872791921243764015->-9010107788625766273 2872791921243764015->5590104336072004446 2872791921243764015->-8679020406282899939 2872791921243764015->4237408165698940119 2872791921243764015->-1248208489229323032 -9027042924522610308 chip.filter -5163501493044317940 SAMstats QC -9027042924522610308->-5163501493044317940 -3279404857355165997 Filt/deduped BAM -9027042924522610308->-3279404857355165997 1725672539077791030 LibCmplx QC -9027042924522610308->1725672539077791030 -3279404857355165997->3241724654863557108 8455969936566217109 chip.jsd -3279404857355165997->8455969936566217109 -1638956813999209428 chip.align -2312268324377227681 SAMstats QC -1638956813999209428->-2312268324377227681 -4836222068589472063 BAM -1638956813999209428->-4836222068589472063 -4836222068589472063->-9027042924522610308 -8244406323080643630 chip.xcor -4625834192728478304 XCOR Plot -8244406323080643630->-4625834192728478304 -2484720213105273040 BW FC -5685839581835457289->-2484720213105273040 5974719186835944655 BW p-val -5685839581835457289->5974719186835944655 -613882069068436438 FASTQ R1 (1) -613882069068436438->-1638956813999209428 -613882069068436438->-8244406323080643630 6593872459071764681 Peak (bfilt) -8893451595391182000->6593872459071764681 8780309035483193882 Peak -8893451595391182000->8780309035483193882 8780309035483193882->-8489622891355707258 8780309035483193882->4551850613035248723 8780309035483193882->-8679020406282899939 8780309035483193882->4237408165698940119 -4300975068536731746 chip.bam2ta -943202089445349470 TAG-ALIGN -4300975068536731746->-943202089445349470 -943202089445349470->6866839613220246045 -943202089445349470->4365031997116084313 -943202089445349470->-5685839581835457289 -943202089445349470->-8893451595391182000 -943202089445349470->-9010107788625766273 -943202089445349470->5590104336072004446 -943202089445349470->-8679020406282899939 -943202089445349470->4237408165698940119 -943202089445349470->-1248208489229323032 -1951568503543298856 chip.filter -8547734548037954799 SAMstats QC -1951568503543298856->-8547734548037954799 5062347699187147169 Filt/deduped BAM -1951568503543298856->5062347699187147169 172331512757392715 LibCmplx QC -1951568503543298856->172331512757392715 5062347699187147169->-4300975068536731746 5062347699187147169->8455969936566217109 708319100622192853 chip.align 6094891561073795959 SAMstats QC 708319100622192853->6094891561073795959 -7783622768861550036 BAM 708319100622192853->-7783622768861550036 -7783622768861550036->-1951568503543298856 -3200642418338305249 chip.xcor 1006925631896717102 XCOR Plot -3200642418338305249->1006925631896717102 5943431565942154459 BW p-val -9010107788625766273->5943431565942154459 5447687407167425895 BW FC -9010107788625766273->5447687407167425895 1131363898935320965 FASTQ R1 (1) 1131363898935320965->708319100622192853 1131363898935320965->-3200642418338305249 3714246662954287534 chip.pool_ta_ctl 2320599906551970079 TAG-ALIGN 3714246662954287534->2320599906551970079 2320599906551970079->2382572364002699489 2320599906551970079->-4365252832810290087 2320599906551970079->4365031997116084313 2320599906551970079->-5685839581835457289 2320599906551970079->-8893451595391182000 2320599906551970079->-9010107788625766273 2320599906551970079->5590104336072004446 2320599906551970079->-8679020406282899939 2320599906551970079->4237408165698940119 2320599906551970079->-1248208489229323032 -2062376758149184109 chip.bam2ta_ctl -8866511294762633610 TAG-ALIGN -2062376758149184109->-8866511294762633610 -8866511294762633610->4365031997116084313 -8866511294762633610->-5685839581835457289 -8866511294762633610->-8893451595391182000 -8866511294762633610->-9010107788625766273 -8866511294762633610->3714246662954287534 -8866511294762633610->-8679020406282899939 -8866511294762633610->4237408165698940119 4141400869298128343 chip.filter_ctl 7187246854952404012 SAMstats QC 4141400869298128343->7187246854952404012 7668630549010542925 Filt/deduped BAM 4141400869298128343->7668630549010542925 8989283476278863963 LibCmplx QC 4141400869298128343->8989283476278863963 7668630549010542925->-2062376758149184109 7668630549010542925->8455969936566217109 -803103855296124524 chip.align_ctl 2945144720726291301 SAMstats QC -803103855296124524->2945144720726291301 8573790050571202591 BAM -803103855296124524->8573790050571202591 8573790050571202591->4141400869298128343 -1080221327962302441 FASTQ R1 (1) -1080221327962302441->-803103855296124524 -8788166650882222899 chip.bam2ta_ctl -5114681077449782894 TAG-ALIGN -8788166650882222899->-5114681077449782894 -5114681077449782894->4365031997116084313 -5114681077449782894->-5685839581835457289 -5114681077449782894->-8893451595391182000 -5114681077449782894->-9010107788625766273 -5114681077449782894->3714246662954287534 -5114681077449782894->-8679020406282899939 -5114681077449782894->4237408165698940119 -7236009489955642238 chip.filter_ctl 1015878328443967562 SAMstats QC -7236009489955642238->1015878328443967562 1844132554032182476 Filt/deduped BAM -7236009489955642238->1844132554032182476 -4260774291501324248 LibCmplx QC -7236009489955642238->-4260774291501324248 1844132554032182476->-8788166650882222899 1844132554032182476->8455969936566217109 -5946838312145240080 chip.align_ctl -5384477977782957792 SAMstats QC -5946838312145240080->-5384477977782957792 7456813258774329553 BAM -5946838312145240080->7456813258774329553 7456813258774329553->-7236009489955642238 6467292752062196269 FASTQ R1 (1) 6467292752062196269->-5946838312145240080 7920414171769612667 IDR Plot ppr 5590104336072004446->7920414171769612667 5115825460532453970 IDR Peak ppr 5590104336072004446->5115825460532453970 5115825460532453970->4237408165698940119 -970406287663773245 IDR Plot rep1_vs_rep2 -8489622891355707258->-970406287663773245 -6130667911192485748 IDR NPeak rep1_vs_rep2 -8489622891355707258->-6130667911192485748 -6130667911192485748->4237408165698940119 -6515290391227251950 Overlap Peak rep1_vs_rep2 4551850613035248723->-6515290391227251950 -6515290391227251950->-8679020406282899939 -2708722640908354901 Overlap Peak optimal -8679020406282899939->-2708722640908354901 -6123190017143822298 Overlap reproducibility -8679020406282899939->-6123190017143822298 8269184813235716898 IDR Peak optimal 4237408165698940119->8269184813235716898 8600616900309282750 IDR reproducibility 4237408165698940119->8600616900309282750 -1825794829983848072 Overlap Peak ppr -1248208489229323032->-1825794829983848072 -1825794829983848072->-8679020406282899939 -765374543802420405 JSD Plot 8455969936566217109->-765374543802420405

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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