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.H/align/rep1/pseudorep1/encode_2024.LV.macrophage.H.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/align/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/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.H/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.H/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.H/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.H/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.H/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.H/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.H/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.H/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.H/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.H/peak/rep1/pseudorep1/encode_2024.LV.macrophage.H.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep1/encode_2024.LV.macrophage.H.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep1/encode_2024.LV.macrophage.H.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep1/encode_2024.LV.macrophage.H.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep1/encode_2024.LV.macrophage.H.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/encode_2024.LV.macrophage.H.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/encode_2024.LV.macrophage.H.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/encode_2024.LV.macrophage.H.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/encode_2024.LV.macrophage.H.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/peak/rep1/encode_2024.LV.macrophage.H.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.H/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.H/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.H/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.H/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.H/qc/rep1/pseudorep1/encode_2024.LV.macrophage.H.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.H/qc/rep1/pseudorep2/encode_2024.LV.macrophage.H.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/qc/rep1/encode_2024.LV.macrophage.H.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/signal/rep1/encode_2024.LV.macrophage.H.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.H/signal/rep1/encode_2024.LV.macrophage.H.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 -8232204060349767181 macs2_signal_track -8551979844863581149 BW FC -8232204060349767181->-8551979844863581149 -1378385553271175300 BW p-val -8232204060349767181->-1378385553271175300 2241659147415260873 call_peak -6441278666257798895 Peak (bfilt) 2241659147415260873->-6441278666257798895 1065780435620563681 Peak 2241659147415260873->1065780435620563681 3586758082433636759 reproducibility_overlap 1065780435620563681->3586758082433636759 -6100953728596273395 reproducibility_idr 1065780435620563681->-6100953728596273395 6609769004054288962 TAG-ALIGN 6609769004054288962->-8232204060349767181 6609769004054288962->2241659147415260873 6609769004054288962->3586758082433636759 6609769004054288962->-6100953728596273395 6620420632771767990 Overlap Peak optimal 3586758082433636759->6620420632771767990 5358886746758455838 Overlap reproducibility 3586758082433636759->5358886746758455838 -6248823623196251109 IDR Peak optimal -6100953728596273395->-6248823623196251109 5188472119972233103 IDR reproducibility -6100953728596273395->5188472119972233103