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Report generated at 2020-07-14 09:53:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63884456	53978528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59925733	49170794
Mapped(QC-failed)	0	0
% Mapped	93.8000	91.0900
Paired	63884456	53978528
Paired(QC-failed)	0	0
Read1	31942228	26989264
Read1(QC-failed)	0	0
Read2	31942228	26989264
Read2(QC-failed)	0	0
Properly Paired	57069669	47390120
Properly Paired(QC-failed)	0	0
% Properly Paired	89.3300	87.7900
With itself	58841375	48351210
With itself(QC-failed)	0	0
Singletons	1084358	819584
Singletons(QC-failed)	0	0
% Singleton	1.7000	1.5200
Diff. Chroms	1331461	552130
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	25313241	19556389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	336880	746028
Paired Opt. Dupes	5088	2627
% Dupes/100	0.0133	0.0381

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	25313106	19556328
Distinct Read Pairs	24976226	18810303
One Read Pair	24642816	18088069
Two Read Pairs	329971	699092
NRF = Distinct/Total	0.9867	0.9619
PBC1 = OnePair/Distinct	0.9867	0.9616
PBC2 = OnePair/TwoPair	74.6818	25.8737

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	49952722	37620722
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49952722	37620722
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49952722	37620722
Paired(QC-failed)	0	0
Read1	24976361	18810361
Read1(QC-failed)	0	0
Read2	24976361	18810361
Read2(QC-failed)	0	0
Properly Paired	49952722	37620722
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49952722	37620722
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	112142
Np	0
N optimal	112142
N conservative	112142
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.	260
Corr. Est. Fragment Len.	0.2519
Phantom Peak	50
Corr. Phantom Peak	0.2312
Argmin. Corr.	1500
Min. Corr.	0.2069
NSC	1.2176
RSC	1.8531

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	0.4424

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	0.0824
AUC	0.4942
CHANCE divergence	0.4999
Elbow Point	0.0000
JS Distance	0.7793
Synthetic AUC	0.4946
Synthetic Elbow Point	0.2019
Synthetic JS Distance	0.5160