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Report generated at 2020-07-07 19:03:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81115004	191368600
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79737497	188343604
Mapped(QC-failed)	0	0
% Mapped	98.3000	98.4200
Paired	81115004	191368600
Paired(QC-failed)	0	0
Read1	40557502	95684300
Read1(QC-failed)	0	0
Read2	40557502	95684300
Read2(QC-failed)	0	0
Properly Paired	79313880	184873296
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7800	96.6100
With itself	79438248	187197664
With itself(QC-failed)	0	0
Singletons	299249	1145940
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.6000
Diff. Chroms	22194	115130
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	36153113	81954369
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4217888	829023
Paired Opt. Dupes	2004	3469
% Dupes/100	0.1167	0.0101

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36120001	81835994
Distinct Read Pairs	31907524	81045982
One Read Pair	28218383	80287109
Two Read Pairs	3286934	744300
NRF = Distinct/Total	0.8834	0.9903
PBC1 = OnePair/Distinct	0.8844	0.9906
PBC2 = OnePair/TwoPair	8.5850	107.8693

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	63870450	162250692
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63870450	162250692
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63870450	162250692
Paired(QC-failed)	0	0
Read1	31935225	81125346
Read1(QC-failed)	0	0
Read2	31935225	81125346
Read2(QC-failed)	0	0
Properly Paired	63870450	162250692
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63870450	162250692
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	45812
Np	0
N optimal	45812
N conservative	45812
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.	180
Corr. Est. Fragment Len.	0.2271
Phantom Peak	50
Corr. Phantom Peak	0.1819
Argmin. Corr.	1500
Min. Corr.	0.1531
NSC	1.4839
RSC	2.5667

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	0.3562

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	0.1985
AUC	0.4949
CHANCE divergence	0.1181
Elbow Point	0.0000
JS Distance	0.7682
Synthetic AUC	0.5013
Synthetic Elbow Point	0.3611
Synthetic JS Distance	0.4499