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Report generated at 2020-06-05 19:23:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	102139436	117734680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98676986	114419479
Mapped(QC-failed)	0	0
% Mapped	96.6100	97.1800
Paired	102139436	117734680
Paired(QC-failed)	0	0
Read1	51069718	58867340
Read1(QC-failed)	0	0
Read2	51069718	58867340
Read2(QC-failed)	0	0
Properly Paired	97198341	106794783
Properly Paired(QC-failed)	0	0
% Properly Paired	95.1600	90.7100
With itself	97761419	112779344
With itself(QC-failed)	0	0
Singletons	915567	1640135
Singletons(QC-failed)	0	0
% Singleton	0.9000	1.3900
Diff. Chroms	188124	4519328
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	42296625	44870934
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4610006	32326448
Paired Opt. Dupes	2927	5830
% Dupes/100	0.1090	0.7204

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42295119	44833836
Distinct Read Pairs	37685261	12532121
One Read Pair	33531395	4646556
Two Read Pairs	3741595	1813934
NRF = Distinct/Total	0.8910	0.2795
PBC1 = OnePair/Distinct	0.8898	0.3708
PBC2 = OnePair/TwoPair	8.9618	2.5616

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	75373238	25088972
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75373238	25088972
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75373238	25088972
Paired(QC-failed)	0	0
Read1	37686619	12544486
Read1(QC-failed)	0	0
Read2	37686619	12544486
Read2(QC-failed)	0	0
Properly Paired	75373238	25088972
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75373238	25088972
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	27587
Np	0
N optimal	27587
N conservative	27587
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.	140
Corr. Est. Fragment Len.	0.1766
Phantom Peak	50
Corr. Phantom Peak	0.1872
Argmin. Corr.	1500
Min. Corr.	0.1672
NSC	1.0565
RSC	0.4727

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	0.0636

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	0.3004
AUC	0.4953
CHANCE divergence	0.1095
Elbow Point	0.0000
JS Distance	0.5527
Synthetic AUC	0.4993
Synthetic Elbow Point	0.0970
Synthetic JS Distance	0.2535