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Report generated at 2020-06-06 07:57:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120176822	121716226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117811484	120134777
Mapped(QC-failed)	0	0
% Mapped	98.0300	98.7000
Paired	120176822	121716226
Paired(QC-failed)	0	0
Read1	60088411	60858113
Read1(QC-failed)	0	0
Read2	60088411	60858113
Read2(QC-failed)	0	0
Properly Paired	116414711	118947303
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8700	97.7300
With itself	117002135	119535099
With itself(QC-failed)	0	0
Singletons	809349	599678
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.4900
Diff. Chroms	219559	121425
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	52238957	52668443
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4527501	2441741
Paired Opt. Dupes	11184	11372
% Dupes/100	0.0867	0.0464

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52238236	52600749
Distinct Read Pairs	47710805	50164652
One Read Pair	43557469	47837615
Two Read Pairs	3808790	2226928
NRF = Distinct/Total	0.9133	0.9537
PBC1 = OnePair/Distinct	0.9129	0.9536
PBC2 = OnePair/TwoPair	11.4360	21.4814

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	95422912	100453404
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95422912	100453404
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	95422912	100453404
Paired(QC-failed)	0	0
Read1	47711456	50226702
Read1(QC-failed)	0	0
Read2	47711456	50226702
Read2(QC-failed)	0	0
Properly Paired	95422912	100453404
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	95422912	100453404
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	139173
Np	0
N optimal	139173
N conservative	139173
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.	210
Corr. Est. Fragment Len.	0.1907
Phantom Peak	50
Corr. Phantom Peak	0.1904
Argmin. Corr.	1500
Min. Corr.	0.1782
NSC	1.0702
RSC	1.0252

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	0.4695

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	0.1791
AUC	0.4958
CHANCE divergence	0.1240
Elbow Point	0.0000
JS Distance	0.7834
Synthetic AUC	0.4978
Synthetic Elbow Point	0.3164
Synthetic JS Distance	0.4526