File table
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FilesPath
Alignment
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/align/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/align/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/peak/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/roussos_2024.KCl.6hr.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/roussos_2024.KCl.6hr.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/roussos_2024.KCl.6hr.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/roussos_2024.KCl.6hr.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/peak/rep1/roussos_2024.KCl.6hr.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.6hr/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.6hr/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.6hr/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.6hr/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.6hr/qc/rep1/pseudorep1/roussos_2024.KCl.6hr.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/qc/rep1/pseudorep2/roussos_2024.KCl.6hr.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/qc/rep1/roussos_2024.KCl.6hr.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/signal/rep1/roussos_2024.KCl.6hr.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.KCl.6hr/signal/rep1/roussos_2024.KCl.6hr.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 1259177660023196155 macs2_signal_track 5254401486339915552 BW FC 1259177660023196155->5254401486339915552 8229274138213867495 BW p-val 1259177660023196155->8229274138213867495 -9199689965733447957 call_peak 6039730868545783679 Peak (bfilt) -9199689965733447957->6039730868545783679 -6987508842772268407 Peak -9199689965733447957->-6987508842772268407 5689409682071700273 reproducibility_overlap -6987508842772268407->5689409682071700273 -8024046493629249063 reproducibility_idr -6987508842772268407->-8024046493629249063 -6679341338788286929 TAG-ALIGN -6679341338788286929->1259177660023196155 -6679341338788286929->-9199689965733447957 -6679341338788286929->5689409682071700273 -6679341338788286929->-8024046493629249063 4396845163067107022 Overlap Peak optimal 5689409682071700273->4396845163067107022 1476528633171050134 Overlap reproducibility 5689409682071700273->1476528633171050134 -64019525802426939 IDR Peak optimal -8024046493629249063->-64019525802426939 9214237597720966086 IDR reproducibility -8024046493629249063->9214237597720966086