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Pipeline version: v1.1.7

Report generated at 2019-10-28 17:23:21

Paired-end: True

Pipeline type: TF ChIP-Seq

Genome: hg19_klab.tsv

Peak caller: SPP

Alignment

Flagstat (raw BAM)

	rep1	rep2	ctl1
Total	25232058	18152438	16644512
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	23922205	16551414	14322086
Mapped(QC-failed)	0	0	0
% Mapped	94.8100	91.1800	86.0500
Paired	25232058	18152438	16644512
Paired(QC-failed)	0	0	0
Read1	12616029	9076219	8322256
Read1(QC-failed)	0	0	0
Read2	12616029	9076219	8322256
Read2(QC-failed)	0	0	0
Properly Paired	22487276	15524111	13267501
Properly Paired(QC-failed)	0	0	0
% Properly Paired	89.1200	85.5200	79.7100
With itself	23550965	16186035	14012977
With itself(QC-failed)	0	0	0
Singletons	371240	365379	309109
Singletons(QC-failed)	0	0	0
% Singleton	1.4700	2.0100	1.8600
Diff. Chroms	524688	234803	203295
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	7193816	5454541	4621801
Unmapped Reads	0	0	0
Unpaired Dupes	0	0	0
Paired Dupes	722421	1302642	1881228
Paired Opt. Dupes	0	0	0
% Dupes/100	0.1004	0.2388	0.4070

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Read Pairs	6326644	5082079	4586455
Distinct Read Pairs	6274063	4040896	2721330
One Read Pair	6222427	3185527	1521852
Two Read Pairs	51126	700778	749069
NRF = Distinct/Total	0.9917	0.7951	0.5933
PBC1 = OnePair/Distinct	0.9918	0.7883	0.5592
PBC2 = OnePair/TwoPair	121.7077	4.5457	2.0317

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	12942790	8303798	5481146
Total(QC-failed)	0	0	0
Dupes	0	0	0
Dupes(QC-failed)	0	0	0
Mapped	12942790	8303798	5481146
Mapped(QC-failed)	0	0	0
% Mapped	100.0000	100.0000	100.0000
Paired	12942790	8303798	5481146
Paired(QC-failed)	0	0	0
Read1	6471395	4151899	2740573
Read1(QC-failed)	0	0	0
Read2	6471395	4151899	2740573
Read2(QC-failed)	0	0	0
Properly Paired	12942790	8303798	5481146
Properly Paired(QC-failed)	0	0	0
% Properly Paired	100.0000	100.0000	100.0000
With itself	12942790	8303798	5481146
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	899	14
N1	1170	53
N2	10528	775
Np	1256	215
N optimal	1256	215
N conservative	899	14
Optimal Set	ppr	ppr
Conservative Set	rep1-rep2	rep1-rep2
Rescue Ratio	1.3971	15.3571
Self Consistency Ratio	8.9983	14.6226
Reproducibility	borderline	fail

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	0.0044	0.0043	0.0305	0.0059

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	0.0002	0.0005	0.0060	0.0017

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	0.2060	0.1599
AUC	0.4802	0.4753
CHANCE divergence	0.3625	0.5028
Elbow Point	0.0000	0.0000
JS Distance	0.6577	0.6366
Synthetic AUC	0.5010	0.5025
Synthetic Elbow Point	0.0863	0.0852
Synthetic JS Distance	0.2160	0.2113