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Report generated at 2020-12-04 05:24:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72943044	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72078894	187969057
Mapped(QC-failed)	0	0
% Mapped	98.8200	97.0900
Paired	72943044	193594802
Paired(QC-failed)	0	0
Read1	36471522	96797401
Read1(QC-failed)	0	0
Read2	36471522	96797401
Read2(QC-failed)	0	0
Properly Paired	71572164	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1200	95.1900
With itself	71875133	185784698
With itself(QC-failed)	0	0
Singletons	203761	2184359
Singletons(QC-failed)	0	0
% Singleton	0.2800	1.1300
Diff. Chroms	156379	610670
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	32724762	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1282461	539110
Paired Opt. Dupes	4245	19807
% Dupes/100	0.0392	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32712327	77646644
Distinct Read Pairs	31430442	77172156
One Read Pair	30195079	76701136
Two Read Pairs	1190405	467668
NRF = Distinct/Total	0.9608	0.9939
PBC1 = OnePair/Distinct	0.9607	0.9939
PBC2 = OnePair/TwoPair	25.3654	164.0077

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	62884602	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62884602	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	62884602	155345422
Paired(QC-failed)	0	0
Read1	31442301	77672711
Read1(QC-failed)	0	0
Read2	31442301	77672711
Read2(QC-failed)	0	0
Properly Paired	62884602	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	62884602	155345422
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	118015
Np	0
N optimal	118015
N conservative	118015
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.	240
Corr. Est. Fragment Len.	0.2089
Phantom Peak	50
Corr. Phantom Peak	0.2055
Argmin. Corr.	1500
Min. Corr.	0.1837
NSC	1.1367
RSC	1.1531

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	0.3698

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	0.1910
AUC	0.4949
CHANCE divergence	0.1443
Elbow Point	0.0000
JS Distance	0.7322
Synthetic AUC	0.4986
Synthetic Elbow Point	0.3254
Synthetic JS Distance	0.4255