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Report generated at 2020-07-10 10:09:06

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	87081976	104183442
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85815823	101561725
Mapped(QC-failed)	0	0
% Mapped	98.5500	97.4800
Paired	87081976	104183442
Paired(QC-failed)	0	0
Read1	43540988	52091721
Read1(QC-failed)	0	0
Read2	43540988	52091721
Read2(QC-failed)	0	0
Properly Paired	75361734	83193856
Properly Paired(QC-failed)	0	0
% Properly Paired	86.5400	79.8500
With itself	85149724	100020683
With itself(QC-failed)	0	0
Singletons	666099	1541042
Singletons(QC-failed)	0	0
% Singleton	0.7600	1.4800
Diff. Chroms	8392716	13877524
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	34151886	36259719
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2008163	570314
Paired Opt. Dupes	2436	2544
% Dupes/100	0.0588	0.0157

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34116999	36250789
Distinct Read Pairs	32113173	35680935
One Read Pair	30304421	35127299
Two Read Pairs	1670137	542681
NRF = Distinct/Total	0.9413	0.9843
PBC1 = OnePair/Distinct	0.9437	0.9845
PBC2 = OnePair/TwoPair	18.1449	64.7292

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	64287446	71378810
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64287446	71378810
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64287446	71378810
Paired(QC-failed)	0	0
Read1	32143723	35689405
Read1(QC-failed)	0	0
Read2	32143723	35689405
Read2(QC-failed)	0	0
Properly Paired	64287446	71378810
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64287446	71378810
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	79055
Np	0
N optimal	79055
N conservative	79055
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.	170
Corr. Est. Fragment Len.	0.1989
Phantom Peak	50
Corr. Phantom Peak	0.1757
Argmin. Corr.	1500
Min. Corr.	0.1594
NSC	1.2475
RSC	2.4183

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	0.2726

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	0.2381
AUC	0.4949
CHANCE divergence	0.1111
Elbow Point	0.0000
JS Distance	0.7086
Synthetic AUC	0.5065
Synthetic Elbow Point	0.2494
Synthetic JS Distance	0.3702