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Report generated at 2020-05-28 13:45:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92286334	137672758
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91863572	135411543
Mapped(QC-failed)	0	0
% Mapped	99.5400	98.3600
Paired	92286334	137672758
Paired(QC-failed)	0	0
Read1	46143167	68836379
Read1(QC-failed)	0	0
Read2	46143167	68836379
Read2(QC-failed)	0	0
Properly Paired	91184092	130358651
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8100	94.6900
With itself	91602566	134702187
With itself(QC-failed)	0	0
Singletons	261006	709356
Singletons(QC-failed)	0	0
% Singleton	0.2800	0.5200
Diff. Chroms	46958	242628
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	43582790	57571020
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1306252	552898
Paired Opt. Dupes	1413	2174
% Dupes/100	0.0300	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43559577	57401418
Distinct Read Pairs	42255778	56929860
One Read Pair	41171462	56475460
Two Read Pairs	940686	445030
NRF = Distinct/Total	0.9701	0.9918
PBC1 = OnePair/Distinct	0.9743	0.9920
PBC2 = OnePair/TwoPair	43.7675	126.9026

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	84553076	114036244
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84553076	114036244
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84553076	114036244
Paired(QC-failed)	0	0
Read1	42276538	57018122
Read1(QC-failed)	0	0
Read2	42276538	57018122
Read2(QC-failed)	0	0
Properly Paired	84553076	114036244
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84553076	114036244
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	122143
Np	0
N optimal	122143
N conservative	122143
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.	160
Corr. Est. Fragment Len.	0.2660
Phantom Peak	55
Corr. Phantom Peak	0.2173
Argmin. Corr.	1500
Min. Corr.	0.1873
NSC	1.4199
RSC	2.6225

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	0.6525

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	0.0901
AUC	0.4956
CHANCE divergence	0.2488
Elbow Point	0.0000
JS Distance	0.8467
Synthetic AUC	0.4975
Synthetic Elbow Point	0.4797
Synthetic JS Distance	0.6048