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Report generated at 2019-10-13 10:12:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97545950	107823298
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90522904	102808981
Mapped(QC-failed)	0	0
% Mapped	92.8000	95.3500
Paired	97545950	107823298
Paired(QC-failed)	0	0
Read1	48772975	53911649
Read1(QC-failed)	0	0
Read2	48772975	53911649
Read2(QC-failed)	0	0
Properly Paired	89344566	101046955
Properly Paired(QC-failed)	0	0
% Properly Paired	91.5900	93.7200
With itself	90014750	102222603
With itself(QC-failed)	0	0
Singletons	508154	586378
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5400
Diff. Chroms	108628	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	40093165	44955145
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	15049468	9651370
Paired Opt. Dupes	7741	7508
% Dupes/100	0.3754	0.2147

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40091607	44902840
Distinct Read Pairs	25042690	35263532
One Read Pair	15940245	27974043
Two Read Pairs	5752601	5543562
NRF = Distinct/Total	0.6246	0.7853
PBC1 = OnePair/Distinct	0.6365	0.7933
PBC2 = OnePair/TwoPair	2.7710	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	50087394	70607550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50087394	70607550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50087394	70607550
Paired(QC-failed)	0	0
Read1	25043697	35303775
Read1(QC-failed)	0	0
Read2	25043697	35303775
Read2(QC-failed)	0	0
Properly Paired	50087394	70607550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50087394	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	84818
Np	0
N optimal	84818
N conservative	84818
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.	0.1446
Phantom Peak	50
Corr. Phantom Peak	0.1511
Argmin. Corr.	1500
Min. Corr.	0.1382
NSC	1.0462
RSC	0.4982

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	0.1012

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	0.2691
AUC	0.4942
CHANCE divergence	0.1255
Elbow Point	0.0000
JS Distance	0.5942
Synthetic AUC	0.4983
Synthetic Elbow Point	0.1094
Synthetic JS Distance	0.2844