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Report generated at 2021-03-19 00:06:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	137064656	121174246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	135822649	117800756
Mapped(QC-failed)	0	0
% Mapped	99.0900	97.2200
Paired	137064656	121174246
Paired(QC-failed)	0	0
Read1	68532328	60587123
Read1(QC-failed)	0	0
Read2	68532328	60587123
Read2(QC-failed)	0	0
Properly Paired	126310500	102846930
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1500	84.8800
With itself	135235751	116568407
With itself(QC-failed)	0	0
Singletons	586898	1232349
Singletons(QC-failed)	0	0
% Singleton	0.4300	1.0200
Diff. Chroms	6603366	9653332
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	59278870	45723686
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1192529	412201
Paired Opt. Dupes	2715	1762
% Dupes/100	0.0201	0.0090

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59273704	45718069
Distinct Read Pairs	58081434	45306289
One Read Pair	56962590	44922876
Two Read Pairs	1057480	373109
NRF = Distinct/Total	0.9799	0.9910
PBC1 = OnePair/Distinct	0.9807	0.9915
PBC2 = OnePair/TwoPair	53.8664	120.4015

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	116172682	90622970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116172682	90622970
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	116172682	90622970
Paired(QC-failed)	0	0
Read1	58086341	45311485
Read1(QC-failed)	0	0
Read2	58086341	45311485
Read2(QC-failed)	0	0
Properly Paired	116172682	90622970
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	116172682	90622970
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	251032
Np	0
N optimal	251032
N conservative	251032
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.	150
Corr. Est. Fragment Len.	0.1967
Phantom Peak	55
Corr. Phantom Peak	0.1862
Argmin. Corr.	1500
Min. Corr.	0.1726
NSC	1.1401
RSC	1.7729

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	0.5796

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	0.1392
AUC	0.4962
CHANCE divergence	0.1522
Elbow Point	0.0000
JS Distance	0.7823
Synthetic AUC	0.4981
Synthetic Elbow Point	0.3885
Synthetic JS Distance	0.5182