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Report generated at 2019-12-03 15:30:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	86840224	96981564
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84810523	94057636
Mapped(QC-failed)	0	0
% Mapped	97.6600	96.9900
Paired	86840224	96981564
Paired(QC-failed)	0	0
Read1	43420112	48490782
Read1(QC-failed)	0	0
Read2	43420112	48490782
Read2(QC-failed)	0	0
Properly Paired	83792751	90998199
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4900	93.8300
With itself	84254196	93287611
With itself(QC-failed)	0	0
Singletons	556327	770025
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.7900
Diff. Chroms	132738	205681
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	36987388	40192164
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1559217	554748
Paired Opt. Dupes	15761	11605
% Dupes/100	0.0422	0.0138

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36986952	40177379
Distinct Read Pairs	35427742	39622917
One Read Pair	33931649	39079490
Two Read Pairs	1435518	534171
NRF = Distinct/Total	0.9578	0.9862
PBC1 = OnePair/Distinct	0.9578	0.9863
PBC2 = OnePair/TwoPair	23.6372	73.1591

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	70856342	79274832
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70856342	79274832
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70856342	79274832
Paired(QC-failed)	0	0
Read1	35428171	39637416
Read1(QC-failed)	0	0
Read2	35428171	39637416
Read2(QC-failed)	0	0
Properly Paired	70856342	79274832
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70856342	79274832
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	194461
Np	0
N optimal	194461
N conservative	194461
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.	135
Corr. Est. Fragment Len.	0.1848
Phantom Peak	50
Corr. Phantom Peak	0.1972
Argmin. Corr.	1500
Min. Corr.	0.1794
NSC	1.0299
RSC	0.3008

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	0.3992

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	0.1962
AUC	0.4951
CHANCE divergence	0.1308
Elbow Point	0.0000
JS Distance	0.7437
Synthetic AUC	0.5059
Synthetic Elbow Point	0.2681
Synthetic JS Distance	0.4110