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Report generated at 2019-11-04 00:22:49

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	159773014	186476942
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	157337937	181693684
Mapped(QC-failed)	0	0
% Mapped	98.4800	97.4300
Paired	159773014	186476942
Paired(QC-failed)	0	0
Read1	79886507	93238471
Read1(QC-failed)	0	0
Read2	79886507	93238471
Read2(QC-failed)	0	0
Properly Paired	155159622	178059283
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1100	95.4900
With itself	156514250	180553291
With itself(QC-failed)	0	0
Singletons	823687	1140393
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.6100
Diff. Chroms	381127	425639
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	71145210	78591287
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1367406	1772322
Paired Opt. Dupes	9948	10324
% Dupes/100	0.0192	0.0226

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	71144028	78496784
Distinct Read Pairs	69776652	76728433
One Read Pair	68428640	75011080
Two Read Pairs	1328944	1678659
NRF = Distinct/Total	0.9808	0.9775
PBC1 = OnePair/Distinct	0.9807	0.9776
PBC2 = OnePair/TwoPair	51.4910	44.6851

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	139555608	153637930
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139555608	153637930
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	139555608	153637930
Paired(QC-failed)	0	0
Read1	69777804	76818965
Read1(QC-failed)	0	0
Read2	69777804	76818965
Read2(QC-failed)	0	0
Properly Paired	139555608	153637930
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	139555608	153637930
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	220150
Np	0
N optimal	220150
N conservative	220150
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.	155
Corr. Est. Fragment Len.	0.1807
Phantom Peak	50
Corr. Phantom Peak	0.1828
Argmin. Corr.	1500
Min. Corr.	0.1791
NSC	1.0087
RSC	0.4324

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	0.4541

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	0.1931
AUC	0.4965
CHANCE divergence	0.1110
Elbow Point	0.0000
JS Distance	0.6874
Synthetic AUC	0.5058
Synthetic Elbow Point	0.3124
Synthetic JS Distance	0.4286