Alignment | |
Control 1 | |
Filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/ctl1/ENCFF000YRN.merged.nodup.bam |
Raw BAM from aligner | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/ctl1/ENCFF000YRN.merged.bam |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/ctl1/ENCFF000YRN.merged.nodup.tagAlign.gz |
Control 2 | |
Filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/ctl2/ENCFF000YRC.merged.nodup.bam |
Raw BAM from aligner | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/ctl2/ENCFF000YRC.merged.bam |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/ctl2/ENCFF000YRC.merged.nodup.tagAlign.gz |
Pooled control | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/pooled-ctl/basename_prefix.pooled.tagAlign.gz |
Pooled replicate | |
Pseudoreplicate 1 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/pooled-rep/pseudorep1/basename_prefix.pooled.tagAlign.gz |
Pseudoreplicate 2 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/pooled-rep/pseudorep2/basename_prefix.pooled.tagAlign.gz |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/pooled-rep/basename_prefix.pooled.tagAlign.gz |
Replicate 1 | |
Pseudoreplicate 1 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep1/pseudorep1/ENCFF000YUU.merged.nodup.pr1.tagAlign.gz |
Pseudoreplicate 2 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep1/pseudorep2/ENCFF000YUU.merged.nodup.pr2.tagAlign.gz |
Filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep1/ENCFF000YUU.merged.nodup.bam |
Raw BAM from aligner | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep1/ENCFF000YUU.merged.bam |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep1/ENCFF000YUU.merged.nodup.tagAlign.gz |
Replicate 2 | |
Pseudoreplicate 1 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep2/pseudorep1/ENCFF000YUV.merged.nodup.pr1.tagAlign.gz |
Pseudoreplicate 2 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep2/pseudorep2/ENCFF000YUV.merged.nodup.pr2.tagAlign.gz |
Filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep2/ENCFF000YUV.merged.nodup.bam |
Raw BAM from aligner | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep2/ENCFF000YUV.merged.bam |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep2/ENCFF000YUV.merged.nodup.tagAlign.gz |
Replicate 3 | |
Pseudoreplicate 1 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep3/pseudorep1/ENCFF000YVR.merged.nodup.pr1.tagAlign.gz |
Pseudoreplicate 2 | |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep3/pseudorep2/ENCFF000YVR.merged.nodup.pr2.tagAlign.gz |
Filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep3/ENCFF000YVR.merged.nodup.bam |
Raw BAM from aligner | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep3/ENCFF000YVR.merged.bam |
TAG-ALIGN | /srv/www/kundaje/natprot_chip/ENCSR000EGR/align/rep3/ENCFF000YVR.merged.nodup.tagAlign.gz |
Peak | |
IDR reproducibility | |
Conservative peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/idr_reproducibility/idr.conservative_peak.regionPeak.gz |
Conservative peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/idr_reproducibility/idr.conservative_peak.regionPeak.bb |
Conservative peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/idr_reproducibility/idr.conservative_peak.regionPeak.hammock.gz |
Optimal peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/idr_reproducibility/idr.optimal_peak.regionPeak.gz |
Optimal peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/idr_reproducibility/idr.optimal_peak.regionPeak.bb |
Optimal peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/idr_reproducibility/idr.optimal_peak.regionPeak.hammock.gz |
Overlap reproducibility | |
Conservative peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.gz |
Conservative peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.bb |
Conservative peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/overlap_reproducibility/overlap.conservative_peak.regionPeak.hammock.gz |
Optimal peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.gz |
Optimal peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.bb |
Optimal peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/overlap_reproducibility/overlap.optimal_peak.regionPeak.hammock.gz |
Pooled pseudoreplicate 1 vs. 2 | |
Blacklist-filtered IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep1/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz |
Pseudoreplicate 2 | |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/pseudorep2/basename_prefix.pooled_x_basename_prefix.pooled.300K.regionPeak.gz |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.gz |
Blacklist-filtered IDR peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.bb |
Blacklist-filtered IDR peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.regionPeak.hammock.gz |
Blacklist-filtered overlap peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.gz |
Rep1 vs. rep3 | |
Blacklist-filtered IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.idr0.05.bfilt.regionPeak.gz |
Blacklist-filtered IDR peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.idr0.05.bfilt.regionPeak.bb |
Blacklist-filtered IDR peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.idr0.05.bfilt.regionPeak.hammock.gz |
Blacklist-filtered overlap peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1_vs_rep3/rep1_vs_rep3.idr0.05.unthresholded-peaks.txt.gz |
Rep2 vs. rep3 | |
Blacklist-filtered IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.idr0.05.bfilt.regionPeak.gz |
Blacklist-filtered IDR peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.idr0.05.bfilt.regionPeak.bb |
Blacklist-filtered IDR peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.idr0.05.bfilt.regionPeak.hammock.gz |
Blacklist-filtered overlap peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2_vs_rep3/rep2_vs_rep3.idr0.05.unthresholded-peaks.txt.gz |
Replicate 1 | |
Pseudorep 1 vs. pseudorep 2 | |
Blacklist-filtered IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/peak/rep1/pseudorep1/ENCFF000YUU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep1/ENCFF000YUU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep1/ENCFF000YUU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep1/ENCFF000YUU.merged.nodup.pr1_x_ctl_for_rep1.300K.regionPeak.gz |
Pseudoreplicate 2 | |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep2/ENCFF000YUU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep2/ENCFF000YUU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep2/ENCFF000YUU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/pseudorep2/ENCFF000YUU.merged.nodup.pr2_x_ctl_for_rep1.300K.regionPeak.gz |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/ENCFF000YUU.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/ENCFF000YUU.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/ENCFF000YUU.merged.nodup_x_ctl_for_rep1.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep1/ENCFF000YUU.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/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/peak/rep2/pseudorep1/ENCFF000YUV.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep1/ENCFF000YUV.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep1/ENCFF000YUV.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep1/ENCFF000YUV.merged.nodup.pr1_x_ctl_for_rep2.300K.regionPeak.gz |
Pseudoreplicate 2 | |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep2/ENCFF000YUV.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep2/ENCFF000YUV.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep2/ENCFF000YUV.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/pseudorep2/ENCFF000YUV.merged.nodup.pr2_x_ctl_for_rep2.300K.regionPeak.gz |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz |
Replicate 3 | |
Pseudorep 1 vs. pseudorep 2 | |
Blacklist-filtered IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.bfilt.regionPeak.gz |
Blacklist-filtered IDR peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.bfilt.regionPeak.bb |
Blacklist-filtered IDR peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.bfilt.regionPeak.hammock.gz |
Blacklist-filtered overlap peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.overlap.bfilt.regionPeak.gz |
Blacklist-filtered overlap peak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.overlap.bfilt.regionPeak.bb |
Blacklist-filtered overlap peak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.overlap.bfilt.regionPeak.hammock.gz |
Unthresholded raw IDR peak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.unthresholded-peaks.txt.gz |
Pseudoreplicate 1 | |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep1/ENCFF000YVR.merged.nodup.pr1_x_ctl_for_rep3.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep1/ENCFF000YVR.merged.nodup.pr1_x_ctl_for_rep3.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep1/ENCFF000YVR.merged.nodup.pr1_x_ctl_for_rep3.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep1/ENCFF000YVR.merged.nodup.pr1_x_ctl_for_rep3.300K.regionPeak.gz |
Pseudoreplicate 2 | |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep2/ENCFF000YVR.merged.nodup.pr2_x_ctl_for_rep3.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep2/ENCFF000YVR.merged.nodup.pr2_x_ctl_for_rep3.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep2/ENCFF000YVR.merged.nodup.pr2_x_ctl_for_rep3.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/pseudorep2/ENCFF000YVR.merged.nodup.pr2_x_ctl_for_rep3.300K.regionPeak.gz |
Blacklist-filtered narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.300K.bfilt.regionPeak.gz |
Blacklist-filtered narrowpeak (BigBed) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.300K.bfilt.regionPeak.bb |
Blacklist-filtered narrowpeak (hammock) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.300K.bfilt.regionPeak.hammock.gz |
Raw narrowpeak | /srv/www/kundaje/natprot_chip/ENCSR000EGR/peak/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.300K.regionPeak.gz |
QC and logs | |
Control 1 | |
Dup QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl1/ENCFF000YRN.merged.dup.qc |
Library complexity QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl1/ENCFF000YRN.merged.lib_complexity.qc |
SAMstats log for Raw BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl1/ENCFF000YRN.merged.samstats.qc |
SAMstats log for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl1/ENCFF000YRN.merged.nodup.samstats.qc |
Control 2 | |
Dup QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl2/ENCFF000YRC.merged.dup.qc |
Library complexity QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl2/ENCFF000YRC.merged.lib_complexity.qc |
SAMstats log for Raw BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl2/ENCFF000YRC.merged.samstats.qc |
SAMstats log for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ctl2/ENCFF000YRC.merged.nodup.samstats.qc |
Pooled pseudoreplicate 1 vs. 2 | |
Fraction of IDR peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/pooled-pseudorep1_vs_2/pooled-pr1_vs_pooled-pr2.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/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/ENCSR000EGR/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.bfilt.frip.qc |
Fraction of overlap peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep2/rep1_vs_rep2.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep2/rep1_vs_rep2.idr0.05.unthresholded-peaks.txt.png |
Rep1 vs. vs vs. rep3 | |
Fraction of IDR peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep3/rep1_vs_rep3.idr0.05.bfilt.frip.qc |
Fraction of overlap peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep3/rep1_vs_rep3.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep3/rep1_vs_rep3.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1_vs_rep3/rep1_vs_rep3.idr0.05.unthresholded-peaks.txt.png |
Rep2 vs. vs vs. rep3 | |
Fraction of IDR peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2_vs_rep3/rep2_vs_rep3.idr0.05.bfilt.frip.qc |
Fraction of overlap peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2_vs_rep3/rep2_vs_rep3.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2_vs_rep3/rep2_vs_rep3.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2_vs_rep3/rep2_vs_rep3.idr0.05.unthresholded-peaks.txt.png |
Replicate 1 | |
Pseudorep 1 vs. pseudorep 2 | |
Fraction of IDR peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/qc/rep1/pseudorep1/ENCFF000YUU.merged.nodup.pr1_x_ctl_for_rep1.300K.bfilt.frip.qc |
Pseudoreplicate 2 | |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/pseudorep2/ENCFF000YUU.merged.nodup.pr2_x_ctl_for_rep1.300K.bfilt.frip.qc |
Cross-correlation Plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png |
Cross-correlation score | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.trim_50bp.filt.no_chrM.15M.cc.qc |
Dup QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.dup.qc |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.nodup_x_ctl_for_rep1.300K.bfilt.frip.qc |
Library complexity QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.lib_complexity.qc |
SAMstats log for Raw BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.samstats.qc |
SAMstats log for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep1/ENCFF000YUU.merged.nodup.samstats.qc |
Replicate 2 | |
Pseudorep 1 vs. pseudorep 2 | |
Fraction of IDR peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2-pseudorep1_vs_2/rep2-pr1_vs_rep2-pr2.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/qc/rep2/pseudorep1/ENCFF000YUV.merged.nodup.pr1_x_ctl_for_rep2.300K.bfilt.frip.qc |
Pseudoreplicate 2 | |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/pseudorep2/ENCFF000YUV.merged.nodup.pr2_x_ctl_for_rep2.300K.bfilt.frip.qc |
Cross-correlation Plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png |
Cross-correlation score | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.trim_50bp.filt.no_chrM.15M.cc.qc |
Dup QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.dup.qc |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.300K.bfilt.frip.qc |
Library complexity QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.lib_complexity.qc |
SAMstats log for Raw BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.samstats.qc |
SAMstats log for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep2/ENCFF000YUV.merged.nodup.samstats.qc |
Replicate 3 | |
Pseudorep 1 vs. pseudorep 2 | |
Fraction of IDR peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.bfilt.frip.qc |
Fraction of overlap peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.overlap.bfilt.frip.qc |
IDR log | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.log |
IDR plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3-pseudorep1_vs_2/rep3-pr1_vs_rep3-pr2.idr0.05.unthresholded-peaks.txt.png |
Pseudoreplicate 1 | |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/pseudorep1/ENCFF000YVR.merged.nodup.pr1_x_ctl_for_rep3.300K.bfilt.frip.qc |
Pseudoreplicate 2 | |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/pseudorep2/ENCFF000YVR.merged.nodup.pr2_x_ctl_for_rep3.300K.bfilt.frip.qc |
Cross-correlation Plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.trim_50bp.filt.no_chrM.15M.cc.plot.png |
Cross-correlation score | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.trim_50bp.filt.no_chrM.15M.cc.qc |
Dup QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.dup.qc |
Fraction of peaks in reads | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.300K.bfilt.frip.qc |
Library complexity QC for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.lib_complexity.qc |
SAMstats log for Raw BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.samstats.qc |
SAMstats log for filtered BAM | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/rep3/ENCFF000YVR.merged.nodup.samstats.qc |
Final HTML report | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/qc.html |
Final QC JSON file | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/qc.json |
Jensen-Shannon distance plot | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/ENCFF000YUU.merged.nodup.jsd_plot.png |
Reproducibility QC for IDR peaks | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/overlap.reproducibility.qc |
Reproducibility QC for overlap peaks | /srv/www/kundaje/natprot_chip/ENCSR000EGR/qc/idr.reproducibility.qc |
Signal | |
Pooled replicate | |
MACS2 signal track (fold-enrichment) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/signal/pooled-rep/basename_prefix.pooled_x_basename_prefix.pooled.fc.signal.bigwig |
MACS2 signal track (p-val) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/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/ENCSR000EGR/signal/rep1/ENCFF000YUU.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig |
MACS2 signal track (p-val) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/signal/rep1/ENCFF000YUU.merged.nodup_x_ctl_for_rep1.pval.signal.bigwig |
Replicate 2 | |
MACS2 signal track (fold-enrichment) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/signal/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.fc.signal.bigwig |
MACS2 signal track (p-val) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/signal/rep2/ENCFF000YUV.merged.nodup_x_ctl_for_rep2.pval.signal.bigwig |
Replicate 3 | |
MACS2 signal track (fold-enrichment) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/signal/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.fc.signal.bigwig |
MACS2 signal track (p-val) | /srv/www/kundaje/natprot_chip/ENCSR000EGR/signal/rep3/ENCFF000YVR.merged.nodup_x_ctl_for_rep3.pval.signal.bigwig |