Alignment | .
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Replicate 1 | .
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Filtered & deduped bam (70M) | ./align/rep1/RBC_I_rep1.sort.nodup.bam
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Bam | ./Chickseq/RBC_I_rep1.sort.bam
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Tag-align | ./align/rep1/RBC_I_rep1.sort.nodup.tagAlign.gz
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Control 1 | .
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Filtered & deduped bam (29M) | ./align/ctl1/RBC_I_contrl.sort.nodup.bam
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Bam | ./Chickseq/RBC_I_contrl.sort.bam
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Tag-align | ./align/ctl1/RBC_I_contrl.sort.nodup.tagAlign.gz
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Pseudo-replicates | .
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Replicate 1 | .
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Pseudo-replicate 1 | .
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Tag-align | ./align/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign.gz
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Pseudo-replicate 2 | .
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Tag-align | ./align/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign.gz
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Signal tracks | .
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MACS2 | .
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Replicate 1 | .
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P-value | ./signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.fc.signal.bw
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Peaks | .
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MACS2 | .
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Replicate 1 | .
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Narrow peak | ./peak/macs2/rep1/RBC_I_rep1.sort.nodup.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Pseudo-replicates | .
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Replicate 1 | .
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Pseudo-replicate 1 | .
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Narrow peak | ./peak/macs2/pseudo_reps/rep1/pr1/RBC_I_rep1.sort.nodup.pr1.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Pseudo-replicate 2 | .
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Narrow peak | ./peak/macs2/pseudo_reps/rep1/pr2/RBC_I_rep1.sort.nodup.pr2.tagAlign_x_RBC_I_contrl.sort.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Naive overlap | .
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Pseudo-replicates | .
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Replicate 1 | .
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Overlapping peak | ./peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
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Optimal set | .
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Overlapping peak | ./peak/macs2/overlap/optimal_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
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Conservative set | .
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Overlapping peak | ./peak/macs2/overlap/conservative_set/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.gz
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QC and logs | .
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Fingerprint JSD Plot | ./qc/rbc_h5_jsd.png
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Replicate 1 | .
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Filtered flagstat log | ./qc/rep1/RBC_I_rep1.sort.nodup.flagstat.qc
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JS Distance | ./qc/rep1/RBC_I_rep1.sort.nodup.jsd.qc
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Dedup. log | ./qc/rep1/RBC_I_rep1.sort.dup.qc
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PBC log | ./qc/rep1/RBC_I_rep1.sort.nodup.pbc.qc
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Cross-corr. log | ./qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.qc
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Cross-corr. plot | ./qc/rep1/RBC_I_rep1.sort.no_chrM.15M.R1.cc.plot.pdf
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Control 1 | .
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Filtered flagstat log | ./qc/ctl1/RBC_I_contrl.sort.nodup.flagstat.qc
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Dedup. log | ./qc/ctl1/RBC_I_contrl.sort.dup.qc
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PBC log | ./qc/ctl1/RBC_I_contrl.sort.nodup.pbc.qc
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Naive overlap | .
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Overlap QC log | ./qc/rbc_h5_peak_overlap_final.qc
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Pseudo-replicates | .
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Replicate 1 | .
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FRiP | ./peak/macs2/overlap/pseudo_reps/rep1/rbc_h5_rep1-pr.naive_overlap.filt.narrowPeak.FRiP.qc
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