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Report generated at 2022-09-02 07:06:12

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	27609396	90540536
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	20524741	89282327
Mapped(QC-failed)	0	0
% Mapped	74.3400	98.6100
Paired	27609396	90540536
Paired(QC-failed)	0	0
Read1	13804698	45270268
Read1(QC-failed)	0	0
Read2	13804698	45270268
Read2(QC-failed)	0	0
Properly Paired	19637132	88688633
Properly Paired(QC-failed)	0	0
% Properly Paired	71.1200	97.9500
With itself	19916311	89002933
With itself(QC-failed)	0	0
Singletons	608430	279394
Singletons(QC-failed)	0	0
% Singleton	2.2000	0.3100
Diff. Chroms	59541	54015
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	7727908	39117707
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3575713	718978
Paired Opt. Dupes	1150	5462
% Dupes/100	0.4627	0.0184

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	7727401	39099565
Distinct Read Pairs	4151792	38381032
One Read Pair	2473736	37680346
Two Read Pairs	850582	685935
NRF = Distinct/Total	0.5373	0.9816
PBC1 = OnePair/Distinct	0.5958	0.9817
PBC2 = OnePair/TwoPair	2.9083	54.9328

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	8304390	76797458
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	8304390	76797458
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	8304390	76797458
Paired(QC-failed)	0	0
Read1	4152195	38398729
Read1(QC-failed)	0	0
Read2	4152195	38398729
Read2(QC-failed)	0	0
Properly Paired	8304390	76797458
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	8304390	76797458
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	38683
Np	0
N optimal	38683
N conservative	38683
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 (10M)

	rep1
Reads	10627110
Est. Fragment Len.	180
Corr. Est. Fragment Len.	0.1184
Phantom Peak	50
Corr. Phantom Peak	0.1530
Argmin. Corr.	1500
Min. Corr.	0.0897
NSC	1.3190
RSC	0.4524

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	0.1347

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	0.1376
AUC	0.4858
CHANCE divergence	0.5262
Elbow Point	0.0000
JS Distance	0.6398
Synthetic AUC	0.5155
Synthetic Elbow Point	0.1692
Synthetic JS Distance	0.3045