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Report generated at 2019-10-12 22:39:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65434854	87587868
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62499409	85042791
Mapped(QC-failed)	0	0
% Mapped	95.5100	97.0900
Paired	65434854	87587868
Paired(QC-failed)	0	0
Read1	32717427	43793934
Read1(QC-failed)	0	0
Read2	32717427	43793934
Read2(QC-failed)	0	0
Properly Paired	61520282	83193525
Properly Paired(QC-failed)	0	0
% Properly Paired	94.0200	94.9800
With itself	61810480	83956805
With itself(QC-failed)	0	0
Singletons	688929	1085986
Singletons(QC-failed)	0	0
% Singleton	1.0500	1.2400
Diff. Chroms	157554	333038
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	27777101	36699350
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4939301	221028
Paired Opt. Dupes	5768	15561
% Dupes/100	0.1778	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27775321	36659304
Distinct Read Pairs	22836318	36439024
One Read Pair	18672756	36223105
Two Read Pairs	3498866	213134
NRF = Distinct/Total	0.8222	0.9940
PBC1 = OnePair/Distinct	0.8177	0.9941
PBC2 = OnePair/TwoPair	5.3368	169.9546

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	45675600	72956644
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45675600	72956644
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45675600	72956644
Paired(QC-failed)	0	0
Read1	22837800	36478322
Read1(QC-failed)	0	0
Read2	22837800	36478322
Read2(QC-failed)	0	0
Properly Paired	45675600	72956644
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45675600	72956644
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	71026
Np	0
N optimal	71026
N conservative	71026
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.	145
Corr. Est. Fragment Len.	0.2017
Phantom Peak	50
Corr. Phantom Peak	0.2008
Argmin. Corr.	1500
Min. Corr.	0.1686
NSC	1.1957
RSC	1.0265

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	0.2519

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	0.2127
AUC	0.4940
CHANCE divergence	0.1450
Elbow Point	0.0000
JS Distance	0.6981
Synthetic AUC	0.5067
Synthetic Elbow Point	0.2636
Synthetic JS Distance	0.3899