Raw reads | .
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Replicate 1 | .
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Fastq (40M) | /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.fastq.gz
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Replicate 2 | .
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Fastq (42M) | /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.fastq.gz
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Control 1 | .
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Fastq (40M) | /mnt/storage/home/psbelokopytova/CNTN6_new_father/fastq/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.fastq.gz
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Alignment | .
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Replicate 1 | .
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Bam (35M) | ./align/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.bam
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Filtered & deduped bam (16M) | ./align/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.bam
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Tag-align | ./align/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.tagAlign.gz
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Replicate 2 | .
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Bam (36M) | ./align/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.bam
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Filtered & deduped bam (16M) | ./align/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.bam
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Tag-align | ./align/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.tagAlign.gz
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Control 1 | .
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Bam (39M) | ./align/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.bam
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Filtered & deduped bam (31M) | ./align/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.bam
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Tag-align | ./align/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.gz
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Pooled replicate | .
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Tag-align | ./align/pooled_rep/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup_pooled.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/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr1.tagAlign.gz
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Pseudo-replicate 2 | .
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Tag-align | ./align/pseudo_reps/rep1/pr2/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr2.tagAlign.gz
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Replicate 2 | .
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Pseudo-replicate 1 | .
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Tag-align | ./align/pseudo_reps/rep2/pr1/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.pr1.tagAlign.gz
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Pseudo-replicate 2 | .
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Tag-align | ./align/pseudo_reps/rep2/pr2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.pr2.tagAlign.gz
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Pooled pseudo-replicates | .
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Pooled pseudo-replicate 1 | .
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Tag-align | ./align/pooled_pseudo_reps/ppr1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr1_pooled.tagAlign.gz
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Pooled pseudo-replicate 2 | .
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Tag-align | ./align/pooled_pseudo_reps/ppr2/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr2_pooled.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/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.fc.signal.bw
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Replicate 2 | .
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P-value | ./signal/macs2/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.fc.signal.bw
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Pooled replicate | .
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P-value | ./signal/macs2/pooled_rep/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup_pooled.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/pooled_rep/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup_pooled.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.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/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Replicate 2 | .
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Narrow peak | ./peak/macs2/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Pooled replicate | .
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Narrow peak | ./peak/macs2/pooled_rep/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup_pooled.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.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/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr1.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.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/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr2.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Replicate 2 | .
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Pseudo-replicate 1 | .
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Narrow peak | ./peak/macs2/pseudo_reps/rep2/pr1/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.pr1.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Pseudo-replicate 2 | .
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Narrow peak | ./peak/macs2/pseudo_reps/rep2/pr2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.pr2.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Pooled pseudo-replicate | .
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Pooled pseudo-replicate 1 | .
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Narrow peak | ./peak/macs2/pooled_pseudo_reps/ppr1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr1_pooled.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Pooled pseudo-replicate 2 | .
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Narrow peak | ./peak/macs2/pooled_pseudo_reps/ppr2/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pr2_pooled.tagAlign_x_P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.tagAlign.pval0.01.500K.narrowPeak.gz
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Naive overlap | .
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True replicates | .
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Rep. 1 vs. Rep. 2 | .
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Overlapping peak | ./peak/macs2/overlap/true_reps/rep1-rep2/cre_K9_rep1-rep2.naive_overlap.filt.narrowPeak.gz
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Pseudo-replicates | .
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Replicate 1 | .
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Overlapping peak | ./peak/macs2/overlap/pseudo_reps/rep1/cre_K9_rep1-pr.naive_overlap.filt.narrowPeak.gz
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Replicate 2 | .
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Overlapping peak | ./peak/macs2/overlap/pseudo_reps/rep2/cre_K9_rep2-pr.naive_overlap.filt.narrowPeak.gz
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Pooled pseudo-replicates | .
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Overlapping peak | ./peak/macs2/overlap/pooled_pseudo_reps/cre_K9_ppr.naive_overlap.filt.narrowPeak.gz
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Optimal set | .
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Overlapping peak | ./peak/macs2/overlap/optimal_set/cre_K9_rep1-rep2.naive_overlap.filt.narrowPeak.gz
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Conservative set | .
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Overlapping peak | ./peak/macs2/overlap/conservative_set/cre_K9_rep1-rep2.naive_overlap.filt.narrowPeak.gz
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QC and logs | .
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Fingerprint JSD Plot | ./qc/cre_K9_jsd.png
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Replicate 1 | .
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Filtered flagstat log | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.flagstat.qc
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JS Distance | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.jsd.qc
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BWA map. flagstat log | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.flagstat.qc
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Dedup. log | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.dup.qc
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PBC log | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.nodup.pbc.qc
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Cross-corr. log | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.no_chrM.15M.cc.qc
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Cross-corr. plot | ./qc/rep1/P381_8_TCCAACTG-TGTGTCAG_L00M_R1_001.no_chrM.15M.cc.plot.pdf
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Replicate 2 | .
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Filtered flagstat log | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.flagstat.qc
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JS Distance | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.jsd.qc
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BWA map. flagstat log | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.flagstat.qc
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Dedup. log | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.dup.qc
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PBC log | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.nodup.pbc.qc
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Cross-corr. log | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.no_chrM.15M.cc.qc
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Cross-corr. plot | ./qc/rep2/P381_9_GACATCTC-TGTCACAC_L00M_R1_001.no_chrM.15M.cc.plot.pdf
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Control 1 | .
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Filtered flagstat log | ./qc/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.flagstat.qc
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BWA map. flagstat log | ./qc/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.flagstat.qc
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Dedup. log | ./qc/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.dup.qc
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PBC log | ./qc/ctl1/P381_1_TCCTGGTA-CAGATCCT_L00M_R1_001.nodup.pbc.qc
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Naive overlap | .
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Overlap QC log | ./qc/cre_K9_peak_overlap_final.qc
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True replicates | .
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Rep. 1 vs. Rep. 2 | .
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FRiP | ./peak/macs2/overlap/true_reps/rep1-rep2/cre_K9_rep1-rep2.naive_overlap.filt.narrowPeak.FRiP.qc
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Pseudo-replicates | .
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Replicate 1 | .
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FRiP | ./peak/macs2/overlap/pseudo_reps/rep1/cre_K9_rep1-pr.naive_overlap.filt.narrowPeak.FRiP.qc
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Replicate 2 | .
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FRiP | ./peak/macs2/overlap/pseudo_reps/rep2/cre_K9_rep2-pr.naive_overlap.filt.narrowPeak.FRiP.qc
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