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Report generated at 2021-12-31 16:28:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	87334890	147967716
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82776628	141073415
Mapped(QC-failed)	0	0
% Mapped	94.7800	95.3400
Paired	87334890	147967716
Paired(QC-failed)	0	0
Read1	43667445	73983858
Read1(QC-failed)	0	0
Read2	43667445	73983858
Read2(QC-failed)	0	0
Properly Paired	78167827	129978073
Properly Paired(QC-failed)	0	0
% Properly Paired	89.5000	87.8400
With itself	81569005	139642816
With itself(QC-failed)	0	0
Singletons	1207623	1430599
Singletons(QC-failed)	0	0
% Singleton	1.3800	0.9700
Diff. Chroms	386907	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	35316080	58170389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6381894	1433825
Paired Opt. Dupes	368	3355
% Dupes/100	0.1807	0.0246

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35280923	58124153
Distinct Read Pairs	28907493	56701457
One Read Pair	23541773	55332829
Two Read Pairs	4529260	1333630
NRF = Distinct/Total	0.8194	0.9755
PBC1 = OnePair/Distinct	0.8144	0.9759
PBC2 = OnePair/TwoPair	5.1977	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	57868372	113473128
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57868372	113473128
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	57868372	113473128
Paired(QC-failed)	0	0
Read1	28934186	56736564
Read1(QC-failed)	0	0
Read2	28934186	56736564
Read2(QC-failed)	0	0
Properly Paired	57868372	113473128
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	57868372	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	61125
Np	0
N optimal	61125
N conservative	61125
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.	0.1891
Phantom Peak	50
Corr. Phantom Peak	0.1742
Argmin. Corr.	1500
Min. Corr.	0.1531
NSC	1.2352
RSC	1.6994

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	0.2350

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	0.2366
AUC	0.4947
CHANCE divergence	0.1188
Elbow Point	0.0000
JS Distance	0.6655
Synthetic AUC	0.5074
Synthetic Elbow Point	0.2654
Synthetic JS Distance	0.3687