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Report generated at 2021-02-05 18:22:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118637450	114964496
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117715685	113057292
Mapped(QC-failed)	0	0
% Mapped	99.2200	98.3400
Paired	118637450	114964496
Paired(QC-failed)	0	0
Read1	59318725	57482248
Read1(QC-failed)	0	0
Read2	59318725	57482248
Read2(QC-failed)	0	0
Properly Paired	115210696	110989369
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1100	96.5400
With itself	117208380	112354296
With itself(QC-failed)	0	0
Singletons	507305	702996
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.6100
Diff. Chroms	71923	166080
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	53465605	48236755
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	527825	258071
Paired Opt. Dupes	17757	15943
% Dupes/100	0.0099	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53456955	48217442
Distinct Read Pairs	52929331	47960279
One Read Pair	52409673	47714915
Two Read Pairs	512296	240532
NRF = Distinct/Total	0.9901	0.9947
PBC1 = OnePair/Distinct	0.9902	0.9949
PBC2 = OnePair/TwoPair	102.3035	198.3724

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	105875560	95957368
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105875560	95957368
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105875560	95957368
Paired(QC-failed)	0	0
Read1	52937780	47978684
Read1(QC-failed)	0	0
Read2	52937780	47978684
Read2(QC-failed)	0	0
Properly Paired	105875560	95957368
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105875560	95957368
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	236892
Np	0
N optimal	236892
N conservative	236892
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.	145
Corr. Est. Fragment Len.	0.1827
Phantom Peak	45
Corr. Phantom Peak	0.1782
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	1.0743
RSC	1.5499

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	0.3694

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	0.2130
AUC	0.4959
CHANCE divergence	0.1128
Elbow Point	0.0000
JS Distance	0.7365
Synthetic AUC	0.5074
Synthetic Elbow Point	0.2116
Synthetic JS Distance	0.3909