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Files	Path
Alignment
Replicate 1
Filtered & deduped bam	./align/rep1/SRR836475.nodup.bam
Fastq
Bam	./align/rep1/SRR836475.bam
Tag-align	./align/rep1/SRR836475.nodup.tagAlign.gz
Control 1
Filtered & deduped bam	./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
Fastq
Bam	./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
Tag-align	./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep1/pr1/SRR836475.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep1/pr2/SRR836475.nodup.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value	./signal/macs2/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw
Fold enrichment	./signal/macs2/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw
Peaks
SPP
Replicate 1
Region peak	./peak/spp/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Region peak	./peak/spp/pseudo_reps/rep1/pr1/SRR836475.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
Pseudo-replicate 2
Region peak	./peak/spp/pseudo_reps/rep1/pr2/SRR836475.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz
Naive overlap
Peak	./peak/SPP/overlap/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz
MACS2
Replicate 1
Narrow peak	./peak/macs2/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak	./peak/macs2/pseudo_reps/rep1/pr1/SRR836475.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
Pseudo-replicate 2
Narrow peak	./peak/macs2/pseudo_reps/rep1/pr2/SRR836475.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz
IDR
Pseudo-replicates
Replicate 1
IDR peak	./peak/idr/pseudo_reps/rep1/SRR836475_rep1-pr.IDR0.05.narrowPeak.gz
QC and logs
Replicate 1
BWA map. flagstat log	./qc/rep1/SRR836475.flagstat.qc
Dedup. log	./qc/rep1/SRR836475.dup.qc
PBC log	./qc/rep1/SRR836475.nodup.pbc.qc
Cross-corr. log	./qc/rep1/SRR836475.nodup.15M.cc.qc
Cross-corr. plot	./qc/rep1/SRR836475.nodup.15M.cc.plot.pdf
Control 1
BWA map. flagstat log	./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.flagstat.qc
Dedup. log	./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc
PBC log	./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc
IDR
IDR QC log	./qc/SRR836475_IDR_final.qc
Pseudo-replicates
Replicate 1
IDR plot	./peak/idr/pseudo_reps/rep1/SRR836475_rep1-pr.unthresholded-peaks.txt.png

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Files

Path

Alignment

Replicate 1

Filtered & deduped bam

./align/rep1/SRR836475.nodup.bam

Fastq

Bam

./align/rep1/SRR836475.bam

Tag-align

./align/rep1/SRR836475.nodup.tagAlign.gz

Control 1

Filtered & deduped bam

./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam

Fastq

Bam

./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam

Tag-align

./align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz

Pseudo-replicates

Replicate 1

Pseudo-replicate 1

Tag-align

./align/pseudo_reps/rep1/pr1/SRR836475.nodup.pr1.tagAlign.gz

Pseudo-replicate 2

Tag-align

./align/pseudo_reps/rep1/pr2/SRR836475.nodup.pr2.tagAlign.gz

Signal tracks

MACS2

Replicate 1

P-value

./signal/macs2/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.pval.signal.bw

Fold enrichment

./signal/macs2/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.fc.signal.bw

Peaks

SPP

Replicate 1

Region peak

./peak/spp/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

Pseudo-replicates

Replicate 1

Pseudo-replicate 1

Region peak

./peak/spp/pseudo_reps/rep1/pr1/SRR836475.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

Pseudo-replicate 2

Region peak

./peak/spp/pseudo_reps/rep1/pr2/SRR836475.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.regionPeak.gz

Naive overlap

Peak

./peak/SPP/overlap/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.naive_overlap.regionPeak.gz

MACS2

Replicate 1

Narrow peak

./peak/macs2/rep1/SRR836475.nodup.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

Pseudo-replicates

Replicate 1

Pseudo-replicate 1

Narrow peak

./peak/macs2/pseudo_reps/rep1/pr1/SRR836475.nodup.pr1.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

Pseudo-replicate 2

Narrow peak

./peak/macs2/pseudo_reps/rep1/pr2/SRR836475.nodup.pr2.tagAlign_x_r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.narrowPeak.gz

IDR

Pseudo-replicates

Replicate 1

IDR peak

./peak/idr/pseudo_reps/rep1/SRR836475_rep1-pr.IDR0.05.narrowPeak.gz

QC and logs

Replicate 1

BWA map. flagstat log

./qc/rep1/SRR836475.flagstat.qc

Dedup. log

./qc/rep1/SRR836475.dup.qc

PBC log

./qc/rep1/SRR836475.nodup.pbc.qc

Cross-corr. log

./qc/rep1/SRR836475.nodup.15M.cc.qc

Cross-corr. plot

./qc/rep1/SRR836475.nodup.15M.cc.plot.pdf

Control 1

BWA map. flagstat log

./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.flagstat.qc

Dedup. log

./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc

PBC log

./qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.pbc.qc

IDR

IDR QC log

./qc/SRR836475_IDR_final.qc

Pseudo-replicates

Replicate 1

IDR plot

./peak/idr/pseudo_reps/rep1/SRR836475_rep1-pr.unthresholded-peaks.txt.png

Flagstat QC (all)

	Reads (QC-passed)	Reads (QC-failed)	Dupes (QC-passed)	Dupes (QC-failed)	Mapped Reads	% Mapped
rep1	34466582	0	0	0	29717029	86.22
ctl1	32022635	0	0	0	21183380	66.15

Dup QC (all)

	Unpaired Reads	Paired Reads	Unmapped Reads	Unpaired Dupes	Paired Dupes	Paired Opt. Dupes	% Dupes
rep1	25823737	0	0	19636679	0	0	0.760412
ctl1	16572675	0	0	13188493	0	0	0.795797

Flagstat QC (all, filtered)

	Reads (QC-passed)	Reads (QC-failed)	Dupes (QC-passed)	Dupes (QC-failed)	Mapped Reads	% Mapped
rep1	6187058	0	0	0	6187058	100.00
ctl1	3384182	0	0	0	3384182	100.00

PBC QC (all)

	Total Read Pairs	Distinct Read Pairs	One Read Pair	Two Read Pairs	NRF = Distinct/Total	PBC1 = OnePair/Distinct	PBC2 = OnePair/TwoPair
rep1	25754449	6866700	2369457	741686	0.266622	0.345065	3.194690
ctl1	16340490	7720329	4661764	1212451	0.472466	0.603830	3.844909

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Cross-correlation QC (all)

	numReads	estFragLen	corr_estFragLen	PhantomPeak	corr_phantomPeak	argmin_corr	min_corr	NSC	RSC
rep1	6181488	165	0.117332105659751	55	0.100576	1500	0.09458856	1.240447	3.798512

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)

SRR836475_IDR_final.qc

Nt	N1	Np	conservative_set	optimal_set	rescue_ratio	self_consistency_ratio	reproducibility
0	189	0	N/A	N/A	NaN	1.0	1