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Report generated at 2019-10-13 10:56:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	101349458	107823298
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96650118	102808981
Mapped(QC-failed)	0	0
% Mapped	95.3600	95.3500
Paired	101349458	107823298
Paired(QC-failed)	0	0
Read1	50674729	53911649
Read1(QC-failed)	0	0
Read2	50674729	53911649
Read2(QC-failed)	0	0
Properly Paired	94998462	101046955
Properly Paired(QC-failed)	0	0
% Properly Paired	93.7300	93.7200
With itself	96026669	102222603
With itself(QC-failed)	0	0
Singletons	623449	586378
Singletons(QC-failed)	0	0
% Singleton	0.6200	0.5400
Diff. Chroms	113600	271557
Diff. Chroms (QC-failed)	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	ctl1
Unpaired Reads	0	0
Paired Reads	42286335	44955145
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	19052417	9651370
Paired Opt. Dupes	6062	7508
% Dupes/100	0.4506	0.2147

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42283682	44902840
Distinct Read Pairs	23232460	35263532
One Read Pair	12274944	27974043
Two Read Pairs	6130004	5543562
NRF = Distinct/Total	0.5494	0.7853
PBC1 = OnePair/Distinct	0.5284	0.7933
PBC2 = OnePair/TwoPair	2.0024	5.0462

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	ctl1
Total	46467836	70607550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46467836	70607550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46467836	70607550
Paired(QC-failed)	0	0
Read1	23233918	35303775
Read1(QC-failed)	0	0
Read2	23233918	35303775
Read2(QC-failed)	0	0
Properly Paired	46467836	70607550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46467836	70607550
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	48171
Np	0
N optimal	48171
N conservative	48171
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	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'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	115
Corr. Est. Fragment Len.	0.1525
Phantom Peak	50
Corr. Phantom Peak	0.1578
Argmin. Corr.	1500
Min. Corr.	0.1404
NSC	1.0863
RSC	0.6956

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

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

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.0914

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)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.2747
AUC	0.4940
CHANCE divergence	0.1280
Elbow Point	0.0000
JS Distance	0.5775
Synthetic AUC	0.5034
Synthetic Elbow Point	0.1211
Synthetic JS Distance	0.2799