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Report generated at 2021-03-18 12:54:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	28500714	121174246
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	23452787	117800756
Mapped(QC-failed)	0	0
% Mapped	82.2900	97.2200
Paired	28500714	121174246
Paired(QC-failed)	0	0
Read1	14250357	60587123
Read1(QC-failed)	0	0
Read2	14250357	60587123
Read2(QC-failed)	0	0
Properly Paired	22564489	102846930
Properly Paired(QC-failed)	0	0
% Properly Paired	79.1700	84.8800
With itself	23274424	116568407
With itself(QC-failed)	0	0
Singletons	178363	1232349
Singletons(QC-failed)	0	0
% Singleton	0.6300	1.0200
Diff. Chroms	61001	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	10343582	45723686
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1219434	412201
Paired Opt. Dupes	809	1762
% Dupes/100	0.1179	0.0090

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	10340615	45718069
Distinct Read Pairs	9121555	45306289
One Read Pair	8059456	44922876
Two Read Pairs	949975	373109
NRF = Distinct/Total	0.8821	0.9910
PBC1 = OnePair/Distinct	0.8836	0.9915
PBC2 = OnePair/TwoPair	8.4839	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	18248296	90622970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	18248296	90622970
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	18248296	90622970
Paired(QC-failed)	0	0
Read1	9124148	45311485
Read1(QC-failed)	0	0
Read2	9124148	45311485
Read2(QC-failed)	0	0
Properly Paired	18248296	90622970
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	18248296	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	55517
Np	0
N optimal	55517
N conservative	55517
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 (11M)

	rep1
Reads	11892417
Est. Fragment Len.	150
Corr. Est. Fragment Len.	0.2009
Phantom Peak	55
Corr. Phantom Peak	0.1539
Argmin. Corr.	1500
Min. Corr.	0.1155
NSC	1.7387
RSC	2.2256

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	0.3233

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	0.1491
AUC	0.4905
CHANCE divergence	0.3511
Elbow Point	0.0000
JS Distance	0.7080
Synthetic AUC	0.5019
Synthetic Elbow Point	0.3284
Synthetic JS Distance	0.4235