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Report generated at 2021-10-23 19:53:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	190644838	219088414
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	172972476	201201418
Mapped(QC-failed)	0	0
% Mapped	90.7300	91.8400
Paired	190644838	219088414
Paired(QC-failed)	0	0
Read1	95322419	109544207
Read1(QC-failed)	0	0
Read2	95322419	109544207
Read2(QC-failed)	0	0
Properly Paired	169269255	195093802
Properly Paired(QC-failed)	0	0
% Properly Paired	88.7900	89.0500
With itself	170765838	198729534
With itself(QC-failed)	0	0
Singletons	2206638	2471884
Singletons(QC-failed)	0	0
% Singleton	1.1600	1.1300
Diff. Chroms	742881	1686556
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	72738990	84750175
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7916378	4543899
Paired Opt. Dupes	13043	16720
% Dupes/100	0.1088	0.0536

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	72738553	84743747
Distinct Read Pairs	64822217	80200171
One Read Pair	57662220	75870816
Two Read Pairs	6469311	4124763
NRF = Distinct/Total	0.8912	0.9464
PBC1 = OnePair/Distinct	0.8895	0.9460
PBC2 = OnePair/TwoPair	8.9132	18.3940

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	129645224	160412552
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129645224	160412552
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	129645224	160412552
Paired(QC-failed)	0	0
Read1	64822612	80206276
Read1(QC-failed)	0	0
Read2	64822612	80206276
Read2(QC-failed)	0	0
Properly Paired	129645224	160412552
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	129645224	160412552
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	105411
Np	0
N optimal	105411
N conservative	105411
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.	110
Corr. Est. Fragment Len.	0.1720
Phantom Peak	50
Corr. Phantom Peak	0.1801
Argmin. Corr.	1500
Min. Corr.	0.1687
NSC	1.0197
RSC	0.2913

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	0.0621

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	0.3049
AUC	0.4964
CHANCE divergence	0.0981
Elbow Point	0.0000
JS Distance	0.5398
Synthetic AUC	0.5043
Synthetic Elbow Point	0.1105
Synthetic JS Distance	0.2433