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Report generated at 2020-07-09 21:51:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92440864	134911976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89568329	131561749
Mapped(QC-failed)	0	0
% Mapped	96.8900	97.5200
Paired	92440864	134911976
Paired(QC-failed)	0	0
Read1	46220432	67455988
Read1(QC-failed)	0	0
Read2	46220432	67455988
Read2(QC-failed)	0	0
Properly Paired	88287209	129326590
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5100	95.8600
With itself	89215942	130892791
With itself(QC-failed)	0	0
Singletons	352387	668958
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5000
Diff. Chroms	595252	887675
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	40262536	56598486
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	178261	240623
Paired Opt. Dupes	1822	1949
% Dupes/100	0.0044	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40260554	56554856
Distinct Read Pairs	40082303	56314799
One Read Pair	39904802	56075865
Two Read Pairs	176753	237833
NRF = Distinct/Total	0.9956	0.9958
PBC1 = OnePair/Distinct	0.9956	0.9958
PBC2 = OnePair/TwoPair	225.7659	235.7783

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	80168550	112715726
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80168550	112715726
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80168550	112715726
Paired(QC-failed)	0	0
Read1	40084275	56357863
Read1(QC-failed)	0	0
Read2	40084275	56357863
Read2(QC-failed)	0	0
Properly Paired	80168550	112715726
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80168550	112715726
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	212864
Np	0
N optimal	212864
N conservative	212864
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.	150
Corr. Est. Fragment Len.	0.1842
Phantom Peak	50
Corr. Phantom Peak	0.1892
Argmin. Corr.	1500
Min. Corr.	0.1757
NSC	1.0481
RSC	0.6260

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	0.2779

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	0.2206
AUC	0.4955
CHANCE divergence	0.1232
Elbow Point	0.0000
JS Distance	0.6757
Synthetic AUC	0.4958
Synthetic Elbow Point	0.2067
Synthetic JS Distance	0.3707