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| Files | Path |
|---|
| Alignment | |
| Replicate 1 | |
| Pseudoreplicate 1 | |
| TAG-ALIGN | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/align/rep1/pseudorep1/trevino_2021.c4.pr1.tagAlign.gz |
| Pseudoreplicate 2 | |
| TAG-ALIGN | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/align/rep1/pseudorep2/trevino_2021.c4.pr2.tagAlign.gz |
| Peak | |
| IDR reproducibility | |
| Conservative peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.gz |
| Conservative peak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.bb |
| Conservative peak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.hammock.gz |
| Conservative peak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.conservative_peak.narrowPeak.starch |
| Optimal peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.gz |
| Optimal peak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.bb |
| Optimal peak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.hammock.gz |
| Optimal peak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/idr_reproducibility/idr.optimal_peak.narrowPeak.starch |
| Overlap reproducibility | |
| Conservative peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.gz |
| Conservative peak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.bb |
| Conservative peak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.hammock.gz |
| Conservative peak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.conservative_peak.narrowPeak.starch |
| Optimal peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.gz |
| Optimal peak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.bb |
| Optimal peak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.hammock.gz |
| Optimal peak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/overlap_reproducibility/overlap.optimal_peak.narrowPeak.starch |
| Replicate 1 | |
| Pseudorep 1 vs. pseudorep 2 | |
| Blacklist-filtered IDR peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/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/trevino_2021/croo/trevino_2021.c4/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/trevino_2021/croo/trevino_2021.c4/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/trevino_2021/croo/trevino_2021.c4/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.starch |
| Blacklist-filtered overlap peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.gz |
| Blacklist-filtered overlap peak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.bb |
| Blacklist-filtered overlap peak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/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/trevino_2021/croo/trevino_2021.c4/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.narrowPeak.starch |
| Unthresholded raw IDR peak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.gz |
| Pseudoreplicate 1 | |
| Blacklist-filtered narrowpeak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep1/trevino_2021.c4.pr1.pval0.01.300K.bfilt.narrowPeak.gz |
| Blacklist-filtered narrowpeak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep1/trevino_2021.c4.pr1.pval0.01.300K.bfilt.narrowPeak.bb |
| Blacklist-filtered narrowpeak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep1/trevino_2021.c4.pr1.pval0.01.300K.bfilt.narrowPeak.hammock.gz |
| Blacklist-filtered narrowpeak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep1/trevino_2021.c4.pr1.pval0.01.300K.bfilt.narrowPeak.starch |
| Raw narrowpeak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep1/trevino_2021.c4.pr1.pval0.01.300K.narrowPeak.gz |
| Pseudoreplicate 2 | |
| Blacklist-filtered narrowpeak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep2/trevino_2021.c4.pr2.pval0.01.300K.bfilt.narrowPeak.gz |
| Blacklist-filtered narrowpeak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep2/trevino_2021.c4.pr2.pval0.01.300K.bfilt.narrowPeak.bb |
| Blacklist-filtered narrowpeak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep2/trevino_2021.c4.pr2.pval0.01.300K.bfilt.narrowPeak.hammock.gz |
| Blacklist-filtered narrowpeak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep2/trevino_2021.c4.pr2.pval0.01.300K.bfilt.narrowPeak.starch |
| Raw narrowpeak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/pseudorep2/trevino_2021.c4.pr2.pval0.01.300K.narrowPeak.gz |
| Blacklist-filtered narrowpeak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/trevino_2021.c4.pval0.01.300K.bfilt.narrowPeak.gz |
| Blacklist-filtered narrowpeak (BigBed) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/trevino_2021.c4.pval0.01.300K.bfilt.narrowPeak.bb |
| Blacklist-filtered narrowpeak (hammock) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/trevino_2021.c4.pval0.01.300K.bfilt.narrowPeak.hammock.gz |
| Blacklist-filtered narrowpeak (starch) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/trevino_2021.c4.pval0.01.300K.bfilt.narrowPeak.starch |
| Raw narrowpeak | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/peak/rep1/trevino_2021.c4.pval0.01.300K.narrowPeak.gz |
| QC and logs | |
| Replicate 1 | |
| Pseudorep 1 vs. pseudorep 2 | |
| Fraction of IDR peaks in reads | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.frip.qc |
| Fraction of overlap peaks in reads | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.overlap.bfilt.frip.qc |
| IDR log | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.log |
| IDR plot | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1-pseudorep1_vs_2/rep1-pr1_vs_rep1-pr2.idr0.05.unthresholded-peaks.txt.png |
| Pseudoreplicate 1 | |
| Fraction of peaks in reads | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1/pseudorep1/trevino_2021.c4.pr1.pval0.01.300K.bfilt.frip.qc |
| Pseudoreplicate 2 | |
| Fraction of peaks in reads | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1/pseudorep2/trevino_2021.c4.pr2.pval0.01.300K.bfilt.frip.qc |
| Fraction of peaks in reads | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/rep1/trevino_2021.c4.pval0.01.300K.bfilt.frip.qc |
| Final HTML report | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/qc.html |
| Final QC JSON file | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/qc.json |
| Reproducibility QC for IDR peaks | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/overlap.reproducibility.qc |
| Reproducibility QC for overlap peaks | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/qc/idr.reproducibility.qc |
| Signal | |
| Replicate 1 | |
| MACS2 signal track (fold-enrichment) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/signal/rep1/trevino_2021.c4.fc.signal.bigwig |
| MACS2 signal track (p-val) | gs://neuro-variants/data/processed/trevino_2021/croo/trevino_2021.c4/signal/rep1/trevino_2021.c4.pval.signal.bigwig |