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Report generated at 2021-06-17 18:42:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65003990	101440092
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63523110	99780498
Mapped(QC-failed)	0	0
% Mapped	97.7200	98.3600
Paired	65003990	101440092
Paired(QC-failed)	0	0
Read1	32501995	50720046
Read1(QC-failed)	0	0
Read2	32501995	50720046
Read2(QC-failed)	0	0
Properly Paired	62883625	95326984
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7400	93.9700
With itself	63217999	99166808
With itself(QC-failed)	0	0
Singletons	305111	613690
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.6000
Diff. Chroms	33206	261884
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	28219169	41234085
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	951854	240099
Paired Opt. Dupes	39941	81824
% Dupes/100	0.0337	0.0058

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28217973	41233472
Distinct Read Pairs	27266156	40993380
One Read Pair	26392351	40758345
Two Read Pairs	818140	231830
NRF = Distinct/Total	0.9663	0.9942
PBC1 = OnePair/Distinct	0.9680	0.9943
PBC2 = OnePair/TwoPair	32.2590	175.8113

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	54534630	81987972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54534630	81987972
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54534630	81987972
Paired(QC-failed)	0	0
Read1	27267315	40993986
Read1(QC-failed)	0	0
Read2	27267315	40993986
Read2(QC-failed)	0	0
Properly Paired	54534630	81987972
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54534630	81987972
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	102701
Np	0
N optimal	102701
N conservative	102701
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.	0.2314
Phantom Peak	55
Corr. Phantom Peak	0.1807
Argmin. Corr.	1500
Min. Corr.	0.1582
NSC	1.4627
RSC	3.2542

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	0.3337

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	0.2089
AUC	0.4943
CHANCE divergence	0.1245
Elbow Point	0.0000
JS Distance	0.7377
Synthetic AUC	0.5104
Synthetic Elbow Point	0.2960
Synthetic JS Distance	0.4124