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Report generated at 2019-11-03 23:05:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	204323764	213968900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	202839195	211195024
Mapped(QC-failed)	0	0
% Mapped	99.2700	98.7000
Paired	204323764	213968900
Paired(QC-failed)	0	0
Read1	102161882	106984450
Read1(QC-failed)	0	0
Read2	102161882	106984450
Read2(QC-failed)	0	0
Properly Paired	200802947	206798914
Properly Paired(QC-failed)	0	0
% Properly Paired	98.2800	96.6500
With itself	201933890	210073494
With itself(QC-failed)	0	0
Singletons	905305	1121530
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5200
Diff. Chroms	555043	2031909
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	93352426	91477404
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4502343	2315030
Paired Opt. Dupes	36958	43440
% Dupes/100	0.0482	0.0253

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	93351747	91372844
Distinct Read Pairs	88849429	89062444
One Read Pair	84529585	86800060
Two Read Pairs	4144308	2218941
NRF = Distinct/Total	0.9518	0.9747
PBC1 = OnePair/Distinct	0.9514	0.9746
PBC2 = OnePair/TwoPair	20.3966	39.1178

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	177700166	178324748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	177700166	178324748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	177700166	178324748
Paired(QC-failed)	0	0
Read1	88850083	89162374
Read1(QC-failed)	0	0
Read2	88850083	89162374
Read2(QC-failed)	0	0
Properly Paired	177700166	178324748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	177700166	178324748
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	240682
Np	0
N optimal	240682
N conservative	240682
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.	175
Corr. Est. Fragment Len.	0.1874
Phantom Peak	50
Corr. Phantom Peak	0.1876
Argmin. Corr.	1500
Min. Corr.	0.1850
NSC	1.0127
RSC	0.9154

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	0.6160

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	0.1501
AUC	0.4969
CHANCE divergence	0.2181
Elbow Point	0.0000
JS Distance	0.6931
Synthetic AUC	0.5035
Synthetic Elbow Point	0.3898
Synthetic JS Distance	0.4827