File table
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FilesPath
Alignment
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/align/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/align/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/peak/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/encode_2024.LV.neuronal.NI.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/encode_2024.LV.neuronal.NI.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/encode_2024.LV.neuronal.NI.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/encode_2024.LV.neuronal.NI.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/peak/rep1/encode_2024.LV.neuronal.NI.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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/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.neuronal.NI/qc/rep1/pseudorep1/encode_2024.LV.neuronal.NI.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/qc/rep1/pseudorep2/encode_2024.LV.neuronal.NI.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/qc/rep1/encode_2024.LV.neuronal.NI.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/signal/rep1/encode_2024.LV.neuronal.NI.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.neuronal.NI/signal/rep1/encode_2024.LV.neuronal.NI.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 6199983036985396180 macs2_signal_track -7933933005861426203 BW FC 6199983036985396180->-7933933005861426203 3780802187421503996 BW p-val 6199983036985396180->3780802187421503996 -6984169559306162955 call_peak -5083655390878590928 Peak (bfilt) -6984169559306162955->-5083655390878590928 -5197314640319180331 Peak -6984169559306162955->-5197314640319180331 -8796919199545489104 reproducibility_overlap -5197314640319180331->-8796919199545489104 8264990539083161674 reproducibility_idr -5197314640319180331->8264990539083161674 2040333202141094449 TAG-ALIGN 2040333202141094449->6199983036985396180 2040333202141094449->-6984169559306162955 2040333202141094449->-8796919199545489104 2040333202141094449->8264990539083161674 5424508266139686825 Overlap Peak optimal -8796919199545489104->5424508266139686825 7655630434409868506 Overlap reproducibility -8796919199545489104->7655630434409868506 2872959405747244296 IDR Peak optimal 8264990539083161674->2872959405747244296 -1245515390671887251 IDR reproducibility 8264990539083161674->-1245515390671887251