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Report generated at 2021-03-19 02:29:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121447132	121174246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118634952	117800756
Mapped(QC-failed)	0	0
% Mapped	97.6800	97.2200
Paired	121447132	121174246
Paired(QC-failed)	0	0
Read1	60723566	60587123
Read1(QC-failed)	0	0
Read2	60723566	60587123
Read2(QC-failed)	0	0
Properly Paired	109371508	102846930
Properly Paired(QC-failed)	0	0
% Properly Paired	90.0600	84.8800
With itself	118039875	116568407
With itself(QC-failed)	0	0
Singletons	595077	1232349
Singletons(QC-failed)	0	0
% Singleton	0.4900	1.0200
Diff. Chroms	5654434	9653332
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	49893738	45723686
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	728055	412201
Paired Opt. Dupes	2212	1762
% Dupes/100	0.0146	0.0090

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49885283	45718069
Distinct Read Pairs	49157827	45306289
One Read Pair	48459289	44922876
Two Read Pairs	678829	373109
NRF = Distinct/Total	0.9854	0.9910
PBC1 = OnePair/Distinct	0.9858	0.9915
PBC2 = OnePair/TwoPair	71.3866	120.4015

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	98331366	90622970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98331366	90622970
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	98331366	90622970
Paired(QC-failed)	0	0
Read1	49165683	45311485
Read1(QC-failed)	0	0
Read2	49165683	45311485
Read2(QC-failed)	0	0
Properly Paired	98331366	90622970
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	98331366	90622970
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	207696
Np	0
N optimal	207696
N conservative	207696
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.	0.1774
Phantom Peak	55
Corr. Phantom Peak	0.1746
Argmin. Corr.	1500
Min. Corr.	0.1709
NSC	1.0384
RSC	1.7443

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	0.1993

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	0.2380
AUC	0.4959
CHANCE divergence	0.1432
Elbow Point	0.0000
JS Distance	0.6060
Synthetic AUC	0.5070
Synthetic Elbow Point	0.1681
Synthetic JS Distance	0.3355