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.NI/align/rep1/pseudorep1/encode_2024.LV.macrophage.NI.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/align/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.NI/peak/rep1/pseudorep1/encode_2024.LV.macrophage.NI.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep1/encode_2024.LV.macrophage.NI.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep1/encode_2024.LV.macrophage.NI.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep1/encode_2024.LV.macrophage.NI.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep1/encode_2024.LV.macrophage.NI.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/encode_2024.LV.macrophage.NI.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/encode_2024.LV.macrophage.NI.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/encode_2024.LV.macrophage.NI.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/encode_2024.LV.macrophage.NI.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/peak/rep1/encode_2024.LV.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.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.macrophage.NI/qc/rep1/pseudorep1/encode_2024.LV.macrophage.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.macrophage.NI/qc/rep1/pseudorep2/encode_2024.LV.macrophage.NI.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/qc/rep1/encode_2024.LV.macrophage.NI.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/signal/rep1/encode_2024.LV.macrophage.NI.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/encode_2024/croo/encode_2024.LV.macrophage.NI/signal/rep1/encode_2024.LV.macrophage.NI.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 744945940927426240 macs2_signal_track 4945955673062356059 BW FC 744945940927426240->4945955673062356059 1809151518520380558 BW p-val 744945940927426240->1809151518520380558 -1221677430232972660 call_peak 1070243743712032822 Peak (bfilt) -1221677430232972660->1070243743712032822 1486915984507143669 Peak -1221677430232972660->1486915984507143669 8466555937752535339 reproducibility_overlap 1486915984507143669->8466555937752535339 3401073919547851259 reproducibility_idr 1486915984507143669->3401073919547851259 -8790889661734345347 TAG-ALIGN -8790889661734345347->744945940927426240 -8790889661734345347->-1221677430232972660 -8790889661734345347->8466555937752535339 -8790889661734345347->3401073919547851259 -7563679837614468602 Overlap Peak optimal 8466555937752535339->-7563679837614468602 -5587466020751510601 Overlap reproducibility 8466555937752535339->-5587466020751510601 3390330180347930210 IDR Peak optimal 3401073919547851259->3390330180347930210 -504380646983259691 IDR reproducibility 3401073919547851259->-504380646983259691