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Report generated at 2022-01-01 00:00:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108900614	110823572
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107910327	109263081
Mapped(QC-failed)	0	0
% Mapped	99.0900	98.5900
Paired	108900614	110823572
Paired(QC-failed)	0	0
Read1	54450307	55411786
Read1(QC-failed)	0	0
Read2	54450307	55411786
Read2(QC-failed)	0	0
Properly Paired	101150492	99432483
Properly Paired(QC-failed)	0	0
% Properly Paired	92.8800	89.7200
With itself	107467627	108603175
With itself(QC-failed)	0	0
Singletons	442700	659906
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.6000
Diff. Chroms	3372388	6017113
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	47478496	44416373
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	840649	432626
Paired Opt. Dupes	1955	1846
% Dupes/100	0.0177	0.0097

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47473775	44406721
Distinct Read Pairs	46633312	43974914
One Read Pair	45843786	43564699
Two Read Pairs	747008	402407
NRF = Distinct/Total	0.9823	0.9903
PBC1 = OnePair/Distinct	0.9831	0.9907
PBC2 = OnePair/TwoPair	61.3699	108.2603

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	93275694	87967494
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	93275694	87967494
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	93275694	87967494
Paired(QC-failed)	0	0
Read1	46637847	43983747
Read1(QC-failed)	0	0
Read2	46637847	43983747
Read2(QC-failed)	0	0
Properly Paired	93275694	87967494
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	93275694	87967494
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	216529
Np	0
N optimal	216529
N conservative	216529
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.	0.1975
Phantom Peak	45
Corr. Phantom Peak	0.1828
Argmin. Corr.	1500
Min. Corr.	0.1737
NSC	1.1370
RSC	2.5967

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	0.5510

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	0.1466
AUC	0.4958
CHANCE divergence	0.1531
Elbow Point	0.0000
JS Distance	0.7820
Synthetic AUC	0.4999
Synthetic Elbow Point	0.3745
Synthetic JS Distance	0.5018