File table
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FilesPath
Alignment
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/align/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/align/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.starch
Replicate 1
Pseudorep 1 vs. pseudorep 2
Blacklist-filtered IDR peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.starch
Blacklist-filtered overlap peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.gz
Blacklist-filtered overlap peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.bb
Blacklist-filtered overlap peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.starch
Unthresholded raw IDR peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/encode_2024.LV.macrophage.I.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/encode_2024.LV.macrophage.I.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/encode_2024.LV.macrophage.I.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/encode_2024.LV.macrophage.I.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/peak/rep1/encode_2024.LV.macrophage.I.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/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc
IDR loggs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plotgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/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/encode_2024/croo/encode_2024.LV.macrophage.I/qc/rep1/pseudorep1/encode_2024.LV.macrophage.I.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/rep1/pseudorep2/encode_2024.LV.macrophage.I.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/rep1/encode_2024.LV.macrophage.I.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/signal/rep1/encode_2024.LV.macrophage.I.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.I/signal/rep1/encode_2024.LV.macrophage.I.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 -3116512248596873921 macs2_signal_track 177392656896384597 BW FC -3116512248596873921->177392656896384597 -680278831612034042 BW p-val -3116512248596873921->-680278831612034042 202851010072402413 call_peak 3410745160197278349 Peak (bfilt) 202851010072402413->3410745160197278349 -1999969173595320224 Peak 202851010072402413->-1999969173595320224 4519548291116684434 reproducibility_overlap -1999969173595320224->4519548291116684434 -1979688706585781937 reproducibility_idr -1999969173595320224->-1979688706585781937 2047590328620506188 TAG-ALIGN 2047590328620506188->-3116512248596873921 2047590328620506188->202851010072402413 2047590328620506188->4519548291116684434 2047590328620506188->-1979688706585781937 4773097175243032514 Overlap Peak optimal 4519548291116684434->4773097175243032514 -2221902207906667290 Overlap reproducibility 4519548291116684434->-2221902207906667290 -3604700014314352219 IDR Peak optimal -1979688706585781937->-3604700014314352219 1015563754819425165 IDR reproducibility -1979688706585781937->1015563754819425165