File table
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FilesPath
Alignment
Replicate 1
Pseudoreplicate 1
TAG-ALIGNgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/align/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.tagAlign.gz
Pseudoreplicate 2
TAG-ALIGNgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/align/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.tagAlign.gz
Peak
IDR reproducibility
Conservative peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch
Overlap reproducibility
Conservative peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz
Conservative peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb
Conservative peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz
Conservative peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch
Optimal peakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz
Optimal peak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb
Optimal peak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz
Optimal peak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/peak/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.pval0.01.300K.narrowPeak.gz
Pseudoreplicate 2
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.pval0.01.300K.narrowPeak.gz
Blacklist-filtered narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/roussos_2024.childhood.Microglia.pval0.01.300K.bfilt.narrowPeak.gz
Blacklist-filtered narrowpeak (BigBed)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/roussos_2024.childhood.Microglia.pval0.01.300K.bfilt.narrowPeak.bb
Blacklist-filtered narrowpeak (hammock)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/roussos_2024.childhood.Microglia.pval0.01.300K.bfilt.narrowPeak.hammock.gz
Blacklist-filtered narrowpeak (starch)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/roussos_2024.childhood.Microglia.pval0.01.300K.bfilt.narrowPeak.starch
Raw narrowpeakgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/peak/rep1/roussos_2024.childhood.Microglia.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.childhood.Microglia/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.childhood.Microglia/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.childhood.Microglia/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log
IDR plotgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/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.childhood.Microglia/qc/rep1/pseudorep1/roussos_2024.childhood.Microglia.pr1.pval0.01.300K.bfilt.frip.qc
Pseudoreplicate 2
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/qc/rep1/pseudorep2/roussos_2024.childhood.Microglia.pr2.pval0.01.300K.bfilt.frip.qc
Fraction of peaks in readsgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/qc/rep1/roussos_2024.childhood.Microglia.pval0.01.300K.bfilt.frip.qc
Final HTML reportgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/qc/qc.html
Final QC JSON filegs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/qc/qc.json
Reproducibility QC for IDR peaksgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/qc/overlap.reproducibility.qc
Reproducibility QC for overlap peaksgs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/qc/idr.reproducibility.qc
Signal
Replicate 1
MACS2 signal track (fold-enrichment)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/signal/rep1/roussos_2024.childhood.Microglia.fc.signal.bigwig
MACS2 signal track (p-val)gs://neuro-variants/data/processed/roussos_2024/croo/roussos_2024.childhood.Microglia/signal/rep1/roussos_2024.childhood.Microglia.pval.signal.bigwig
Task graph
D cluster_rep1 Replicate 1 3612268950407343452 macs2_signal_track -1810642483730727064 BW FC 3612268950407343452->-1810642483730727064 6176473636716889160 BW p-val 3612268950407343452->6176473636716889160 -9014116329861380469 call_peak -6877809220029256394 Peak (bfilt) -9014116329861380469->-6877809220029256394 5686942624599547289 Peak -9014116329861380469->5686942624599547289 -6554309746079747239 reproducibility_overlap 5686942624599547289->-6554309746079747239 6124788467008169056 reproducibility_idr 5686942624599547289->6124788467008169056 -3352318339053017208 TAG-ALIGN -3352318339053017208->3612268950407343452 -3352318339053017208->-9014116329861380469 -3352318339053017208->-6554309746079747239 -3352318339053017208->6124788467008169056 5146644840287988136 Overlap Peak optimal -6554309746079747239->5146644840287988136 -2249481602823812429 Overlap reproducibility -6554309746079747239->-2249481602823812429 1546599136351367650 IDR Peak optimal 6124788467008169056->1546599136351367650 4294836347580442740 IDR reproducibility 6124788467008169056->4294836347580442740