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Report generated at 2019-11-03 11:57:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	127286570	155278814
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125684498	152204810
Mapped(QC-failed)	0	0
% Mapped	98.7400	98.0200
Paired	127286570	155278814
Paired(QC-failed)	0	0
Read1	63643285	77639407
Read1(QC-failed)	0	0
Read2	63643285	77639407
Read2(QC-failed)	0	0
Properly Paired	124459928	149315055
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7800	96.1600
With itself	125195170	151298295
With itself(QC-failed)	0	0
Singletons	489328	906515
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5800
Diff. Chroms	278870	1045401
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	56993040	66029859
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4461206	1524871
Paired Opt. Dupes	12512	14661
% Dupes/100	0.0783	0.0231

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56988335	65968445
Distinct Read Pairs	52527492	64445697
One Read Pair	48360807	62945345
Two Read Pairs	3889617	1479272
NRF = Distinct/Total	0.9217	0.9769
PBC1 = OnePair/Distinct	0.9207	0.9767
PBC2 = OnePair/TwoPair	12.4333	42.5516

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	105063668	129009976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105063668	129009976
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105063668	129009976
Paired(QC-failed)	0	0
Read1	52531834	64504988
Read1(QC-failed)	0	0
Read2	52531834	64504988
Read2(QC-failed)	0	0
Properly Paired	105063668	129009976
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105063668	129009976
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	82302
Np	0
N optimal	82302
N conservative	82302
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.	185
Corr. Est. Fragment Len.	0.1970
Phantom Peak	50
Corr. Phantom Peak	0.1979
Argmin. Corr.	1500
Min. Corr.	0.1823
NSC	1.0809
RSC	0.9443

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	0.3850

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	0.2141
AUC	0.4960
CHANCE divergence	0.1025
Elbow Point	0.0000
JS Distance	0.7731
Synthetic AUC	0.5034
Synthetic Elbow Point	0.3211
Synthetic JS Distance	0.4129