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Report generated at 2022-01-11 19:21:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56173704	147967716
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53616289	141073415
Mapped(QC-failed)	0	0
% Mapped	95.4500	95.3400
Paired	56173704	147967716
Paired(QC-failed)	0	0
Read1	28086852	73983858
Read1(QC-failed)	0	0
Read2	28086852	73983858
Read2(QC-failed)	0	0
Properly Paired	52141492	129978073
Properly Paired(QC-failed)	0	0
% Properly Paired	92.8200	87.8400
With itself	53145467	139642816
With itself(QC-failed)	0	0
Singletons	470822	1430599
Singletons(QC-failed)	0	0
% Singleton	0.8400	0.9700
Diff. Chroms	341748	4101665
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	23542823	58170389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9166035	1433825
Paired Opt. Dupes	1086	3355
% Dupes/100	0.3893	0.0246

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23535234	58124153
Distinct Read Pairs	14372177	56701457
One Read Pair	8369937	55332829
Two Read Pairs	3890817	1333630
NRF = Distinct/Total	0.6107	0.9755
PBC1 = OnePair/Distinct	0.5824	0.9759
PBC2 = OnePair/TwoPair	2.1512	41.4904

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	28753576	113473128
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28753576	113473128
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	28753576	113473128
Paired(QC-failed)	0	0
Read1	14376788	56736564
Read1(QC-failed)	0	0
Read2	14376788	56736564
Read2(QC-failed)	0	0
Properly Paired	28753576	113473128
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	28753576	113473128
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	100639
Np	0
N optimal	100639
N conservative	100639
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.	0.2077
Phantom Peak	55
Corr. Phantom Peak	0.1550
Argmin. Corr.	1500
Min. Corr.	0.1127
NSC	1.8431
RSC	2.2481

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	0.2822

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	0.1678
AUC	0.4924
CHANCE divergence	0.2843
Elbow Point	0.0000
JS Distance	0.6884
Synthetic AUC	0.4970
Synthetic Elbow Point	0.3171
Synthetic JS Distance	0.4152