Alignment |
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Replicate 1 |
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Filtered & deduped bam | ./align/rep1/SRR1016005.nodup.bam
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Fastq |
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Bam | ./align/rep1/SRR1016005.bam
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Tag-align | ./align/rep1/SRR1016005.nodup.tagAlign.gz
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Replicate 2 |
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Filtered & deduped bam | ./align/rep2/SRR1016008.nodup.bam
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Fastq |
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Bam | ./align/rep2/SRR1016008.bam
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Tag-align | ./align/rep2/SRR1016008.nodup.tagAlign.gz
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Control 1 |
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Filtered & deduped bam | ./align/ctl1/ENCFF001HNC.nodup.bam
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Fastq |
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Bam | ./align/ctl1/ENCFF001HNC.bam
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Tag-align | ./align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
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Pooled replicate |
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Tag-align | ./align/pooled_rep/SRR1016005.nodup_SRR1016008.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/SRR1016005.nodup.pr1.tagAlign.gz
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Pseudo-replicate 2 |
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Tag-align | ./align/pseudo_reps/rep1/pr2/SRR1016005.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/SRR1016008.nodup.pr1.tagAlign.gz
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Pseudo-replicate 2 |
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Tag-align | ./align/pseudo_reps/rep2/pr2/SRR1016008.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/SRR1016005.nodup.pr1_SRR1016008.nodup.pr1.tagAlign.gz
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Pooled pseudo-replicate 2 |
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Tag-align | ./align/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.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/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
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Replicate 2 |
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P-value | ./signal/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
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Pooled replicate |
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P-value | ./signal/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
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Fold enrichment | ./signal/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
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Peaks |
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SPP |
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Pooled Replicate |
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Region peak | ./peak/spp/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
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Replicate 1 |
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Region peak | ./peak/spp/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
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Replicate 2 |
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Region peak | ./peak/spp/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
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Pooled pseudo-replicates |
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Pooled pseudo-replicate 1 |
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Region peak | ./peak/spp/pooled_pseudo_reps/ppr1/SRR1016005.nodup.pr1_SRR1016008.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
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Pooled pseudo-replicate 2 |
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Region peak | ./peak/spp/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.regionPeak.gz
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Naive overlap |
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Peak | ./peak/spp/overlap/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.regionPeak.gz
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MACS2 |
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Replicate 1 |
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Narrow peak | ./peak/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
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Broad peak | ./peak/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
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Gapped peak | ./peak/macs2/rep1/SRR1016005.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
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Replicate 2 |
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Narrow peak | ./peak/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
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Broad peak | ./peak/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
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Gapped peak | ./peak/macs2/rep2/SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
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Pooled replicate |
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Narrow peak | ./peak/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
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Broad peak | ./peak/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
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Gapped peak | ./peak/macs2/pooled_rep/SRR1016005.nodup_SRR1016008.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
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Pooled pseudo-replicate |
|
Pooled pseudo-replicate 1 |
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Broad peak | ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
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Gapped peak | ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
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Pooled pseudo-replicate 2 |
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Narrow peak | ./peak/macs2/pooled_pseudo_reps/ppr2/SRR1016005.nodup.pr2_SRR1016008.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
|
IDR |
|
True replicates |
|
Rep. 1 vs. Rep. 2 |
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IDR peak | ./peak/idr/true_reps/rep1-rep2/POL2RA_rep1-rep2.IDR0.05.filt.narrowPeak.gz
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Pooled pseudo-replicates |
|
IDR peak | ./peak/idr/pooled_pseudo_reps/POL2RA_ppr.IDR0.05.filt.narrowPeak.gz
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Optimal set |
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IDR peak | ./peak/idr/optimal_set/POL2RA_ppr.IDR0.05.filt.narrowPeak.gz
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Conservative set |
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IDR peak | ./peak/idr/conservative_set/POL2RA_rep1-rep2.IDR0.05.filt.narrowPeak.gz
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QC and logs |
|
Replicate 1 |
|
BWA map. flagstat log | ./qc/rep1/SRR1016005.flagstat.qc
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Dedup. log | ./qc/rep1/SRR1016005.dup.qc
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PBC log | ./qc/rep1/SRR1016005.nodup.pbc.qc
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Cross-corr. log | ./qc/rep1/SRR1016005.nodup.15M.cc.qc
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Cross-corr. plot | ./qc/rep1/SRR1016005.nodup.15M.cc.plot.pdf
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Replicate 2 |
|
BWA map. flagstat log | ./qc/rep2/SRR1016008.flagstat.qc
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Dedup. log | ./qc/rep2/SRR1016008.dup.qc
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PBC log | ./qc/rep2/SRR1016008.nodup.pbc.qc
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Cross-corr. log | ./qc/rep2/SRR1016008.nodup.15M.cc.qc
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Cross-corr. plot | ./qc/rep2/SRR1016008.nodup.15M.cc.plot.pdf
|
Control 1 |
|
BWA map. flagstat log | ./qc/ctl1/ENCFF001HNC.flagstat.qc
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Dedup. log | ./qc/ctl1/ENCFF001HNC.dup.qc
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PBC log | ./qc/ctl1/ENCFF001HNC.nodup.pbc.qc
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IDR |
|
IDR QC log | ./qc/POL2RA_IDR_final.qc
|
True replicates |
|
Rep. 1 vs. Rep. 2 |
|
IDR plot | ./peak/idr/true_reps/rep1-rep2/POL2RA_rep1-rep2.unthresholded-peaks.txt.png
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Pooled pseudo-replicates |
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IDR plot | ./peak/idr/pooled_pseudo_reps/POL2RA_ppr.unthresholded-peaks.txt.png
|