Directories and files

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Files	Path
Alignment
Replicate 1
Filtered & deduped bam
Tag-align	./align/rep1/SNAI1_Rep3.nodup.tagAlign.gz
Control 1
Tag-align
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep1/pr1/SNAI1_Rep3.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep1/pr2/SNAI1_Rep3.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value	./signal/macs2/rep1/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep1/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
Peaks
SPP
Replicate 1
Region peak	./peak/spp/rep1/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Region peak	./peak/spp/pseudo_reps/rep1/pr1/SNAI1_Rep3.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Pseudo-replicate 2
Region peak	./peak/spp/pseudo_reps/rep1/pr2/SNAI1_Rep3.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
Naive overlap
Peak	./peak/spp/overlap/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
MACS2
Replicate 1
Narrow peak	./peak/macs2/rep1/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak	./peak/macs2/rep1/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak	./peak/macs2/rep1/SNAI1_Rep3.nodup.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep1/pr1/SNAI1_Rep3.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak	./peak/macs2/pseudo_reps/rep1/pr1/SNAI1_Rep3.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak	./peak/macs2/pseudo_reps/rep1/pr1/SNAI1_Rep3.nodup.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep1/pr2/SNAI1_Rep3.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
Broad peak	./peak/macs2/pseudo_reps/rep1/pr2/SNAI1_Rep3.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
Gapped peak	./peak/macs2/pseudo_reps/rep1/pr2/SNAI1_Rep3.nodup.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
IDR
Pseudo-replicates
Replicate 1
IDR peak	./peak/idr/pseudo_reps/rep1/SNAI1_rep1-pr.IDR0.05.filt.narrowPeak.gz
QC and logs
Replicate 1
Cross-corr. log	./qc/rep1/SNAI1_Rep3.nodup.15M.cc.qc
Cross-corr. plot	./qc/rep1/SNAI1_Rep3.nodup.15M.cc.plot.pdf
IDR
IDR QC log	./qc/SNAI1_IDR_final.qc
Pseudo-replicates
Replicate 1
IDR plot	./peak/idr/pseudo_reps/rep1/SNAI1_rep1-pr.unthresholded-peaks.txt.png

Cross-correlation QC (all)

	numReads	estFragLen	corr_estFragLen	PhantomPeak	corr_phantomPeak	argmin_corr	min_corr	NSC	RSC
rep1	11209706	145	0.142884153904748	50	0.1376016	1500	0.1356693	1.053179	3.733908

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value
Important columns highlighted, but all/whole file can be stored for display

IDR QC (idr)

SNAI1_IDR_final.qc

Nt	N1	N2	Np	conservative_set	optimal_set	rescue_ratio	self_consistency_ratio	reproducibility
0	117	0	0	N/A	N/A	NaN	1.0	1