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Pipeline version: v1.1.7

Report generated at 2019-10-28 07:11:38

Paired-end: True

Pipeline type: TF ChIP-Seq

Genome: hg19_klab.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1	rep2	ctl1
Total	16270578	16068156	10734872
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	15399268	15427112	10253019
Mapped(QC-failed)	0	0	0
% Mapped	94.6400	96.0100	95.5100
Paired	16270578	16068156	10734872
Paired(QC-failed)	0	0	0
Read1	8135289	8034078	5367436
Read1(QC-failed)	0	0	0
Read2	8135289	8034078	5367436
Read2(QC-failed)	0	0	0
Properly Paired	14801082	14895197	9126798
Properly Paired(QC-failed)	0	0	0
% Properly Paired	90.9700	92.7000	85.0200
With itself	15118693	15194400	10077130
With itself(QC-failed)	0	0	0
Singletons	280575	232712	175889
Singletons(QC-failed)	0	0	0
% Singleton	1.7200	1.4500	1.6400
Diff. Chroms	198731	186941	548164
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6059608	6108186	3302547
Unmapped Reads	0	0	0
Unpaired Dupes	0	0	0
Paired Dupes	1600397	1373643	483316
Paired Opt. Dupes	0	0	0
% Dupes/100	0.2641	0.2249	0.1463

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Read Pairs	5988476	6036419	3241519
Distinct Read Pairs	4427904	4702233	2790178
One Read Pair	3286701	3697995	2395581
Two Read Pairs	862427	789143	344501
NRF = Distinct/Total	0.7394	0.7790	0.8608
PBC1 = OnePair/Distinct	0.7423	0.7864	0.8586
PBC2 = OnePair/TwoPair	3.8110	4.6861	6.9538

Mitochondrial reads are filtered out.

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

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	rep2	ctl1
Total	8918422	9469086	5638462
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	8918422	9469086	5638462
Mapped(QC-failed)	0	0	0
% Mapped	100.0000	100.0000	100.0000
Paired	8918422	9469086	5638462
Paired(QC-failed)	0	0	0
Read1	4459211	4734543	2819231
Read1(QC-failed)	0	0	0
Read2	4459211	4734543	2819231
Read2(QC-failed)	0	0	0
Properly Paired	8918422	9469086	5638462
Properly Paired(QC-failed)	0	0	0
% Properly Paired	100.0000	100.0000	100.0000
With itself	8918422	9469086	5638462
With itself(QC-failed)	0	0	0
Singletons	0	0	0
Singletons(QC-failed)	0	0	0
% Singleton	0.0000	0.0000	0.0000
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Peak calling

IDR (Irreproducible Discovery Rate) plots

rep1-rep2

rep1-pr

rep2-pr

ppr

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller SPP

	overlap	IDR
Nt	172890	63002
N1	118791	43902
N2	119728	44890
Np	172473	63470
N optimal	172890	63470
N conservative	172890	63002
Optimal Set	rep1-rep2	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.0024	1.0074
Self Consistency Ratio	1.0079	1.0225
Reproducibility	pass	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

IDR (Irreproducible Discovery Rate) peaks

N1: Replicate 1 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consistent IDR 0.05 peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent IDR 0.05 peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Fraction of reads in overlapping peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.4546	0.4229	0.4174	0.4542

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Fraction of reads in IDR peaks

	rep1-rep2	rep1-pr	rep2-pr	ppr
Fraction of Reads in Peak	0.3248	0.2842	0.2837	0.3260

ppr: IDR peaks comparing pooled pseudo replicates
rep1-pr: IDR peaks comparing pseudoreplicates from replicate 1
rep2-pr: IDR peaks comparing pseudoreplicates from replicate 2
repi-repj: IDR peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1	rep2
% genome enriched	0.0637	0.0647
AUC	0.4763	0.4770
CHANCE divergence	0.6641	0.6559
Elbow Point	0.0000	0.0000
JS Distance	0.7909	0.7807
Synthetic AUC	0.5056	0.4916
Synthetic Elbow Point	0.3388	0.3412
Synthetic JS Distance	0.4541	0.4581