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Report generated at 2020-07-09 15:01:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65609300	132672462
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60452349	130821554
Mapped(QC-failed)	0	0
% Mapped	92.1400	98.6000
Paired	65609300	132672462
Paired(QC-failed)	0	0
Read1	32804650	66336231
Read1(QC-failed)	0	0
Read2	32804650	66336231
Read2(QC-failed)	0	0
Properly Paired	60068962	126755240
Properly Paired(QC-failed)	0	0
% Properly Paired	91.5600	95.5400
With itself	60257485	130259338
With itself(QC-failed)	0	0
Singletons	194864	562216
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.4200
Diff. Chroms	16265	151029
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	27998318	55934859
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2675942	398825
Paired Opt. Dupes	1962	4162
% Dupes/100	0.0956	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27987611	55898619
Distinct Read Pairs	25312870	55504111
One Read Pair	22895210	55132878
Two Read Pairs	2203935	363876
NRF = Distinct/Total	0.9044	0.9929
PBC1 = OnePair/Distinct	0.9045	0.9933
PBC2 = OnePair/TwoPair	10.3883	151.5156

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	50644752	111072068
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50644752	111072068
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50644752	111072068
Paired(QC-failed)	0	0
Read1	25322376	55536034
Read1(QC-failed)	0	0
Read2	25322376	55536034
Read2(QC-failed)	0	0
Properly Paired	50644752	111072068
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50644752	111072068
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	119624
Np	0
N optimal	119624
N conservative	119624
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.	150
Corr. Est. Fragment Len.	0.2034
Phantom Peak	55
Corr. Phantom Peak	0.1766
Argmin. Corr.	1500
Min. Corr.	0.1594
NSC	1.2756
RSC	2.5504

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	0.4030

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	0.1787
AUC	0.4943
CHANCE divergence	0.1547
Elbow Point	0.0000
JS Distance	0.7642
Synthetic AUC	0.5002
Synthetic Elbow Point	0.3377
Synthetic JS Distance	0.4430