File table
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FilesPath
Alignment
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/align/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/align/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.starch
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.gz
Blacklist-filtered IDR peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.bb
Blacklist-filtered IDR peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.hammock.gz
Blacklist-filtered IDR peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.starch
Blacklist-filtered overlap peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.hammock.gz
Blacklist-filtered overlap peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.starch
Unthresholded raw IDR peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.gz
Pseudoreplicate 1
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/roussos_2024.KCl.1hr.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/roussos_2024.KCl.1hr.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/roussos_2024.KCl.1hr.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/roussos_2024.KCl.1hr.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/peak/rep1/roussos_2024.KCl.1hr.pval0.01.300K.narrowPeak.gz
QC and logs
Replicate 1
Pseudorep 1 vs. pseudorep 2
Fraction of IDR peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.frip.qc
Fraction of overlap peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR loggs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plotgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.png
Pseudoreplicate 1
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1/pseudorep1/roussos_2024.KCl.1hr.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1/pseudorep2/roussos_2024.KCl.1hr.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/rep1/roussos_2024.KCl.1hr.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/signal/rep1/roussos_2024.KCl.1hr.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.1hr/signal/rep1/roussos_2024.KCl.1hr.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 -6077619290389562745 macs2_signal_track -5288597157388542656 BW p-val -6077619290389562745->-5288597157388542656 521172715197726606 BW FC -6077619290389562745->521172715197726606 -372474333815319702 call_peak 4269833316348283348 Peak (bfilt) -372474333815319702->4269833316348283348 -8713683292172827239 Peak -372474333815319702->-8713683292172827239 5318536976044996981 reproducibility_overlap -8713683292172827239->5318536976044996981 -3219507506019933566 reproducibility_idr -8713683292172827239->-3219507506019933566 -669586134824891859 TAG-ALIGN -669586134824891859->-6077619290389562745 -669586134824891859->-372474333815319702 -669586134824891859->5318536976044996981 -669586134824891859->-3219507506019933566 3128610560411157553 Overlap Peak optimal 5318536976044996981->3128610560411157553 6339461312229363180 Overlap reproducibility 5318536976044996981->6339461312229363180 5547949007021837736 IDR Peak optimal -3219507506019933566->5547949007021837736 5321364708259258605 IDR reproducibility -3219507506019933566->5321364708259258605