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Report generated at 2019-11-03 08:11:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106744706	158940554
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104561990	157152767
Mapped(QC-failed)	0	0
% Mapped	97.9600	98.8800
Paired	106744706	158940554
Paired(QC-failed)	0	0
Read1	53372353	79470277
Read1(QC-failed)	0	0
Read2	53372353	79470277
Read2(QC-failed)	0	0
Properly Paired	103241311	154442853
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7200	97.1700
With itself	104123529	156399332
With itself(QC-failed)	0	0
Singletons	438461	753435
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.4700
Diff. Chroms	592896	1218211
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	46955112	68222921
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9110428	2746068
Paired Opt. Dupes	15652	28097
% Dupes/100	0.1940	0.0403

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46953463	68139154
Distinct Read Pairs	37843334	65397649
One Read Pair	30210351	62741963
Two Read Pairs	6360592	2573454
NRF = Distinct/Total	0.8060	0.9598
PBC1 = OnePair/Distinct	0.7983	0.9594
PBC2 = OnePair/TwoPair	4.7496	24.3804

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	75689368	130953706
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75689368	130953706
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75689368	130953706
Paired(QC-failed)	0	0
Read1	37844684	65476853
Read1(QC-failed)	0	0
Read2	37844684	65476853
Read2(QC-failed)	0	0
Properly Paired	75689368	130953706
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75689368	130953706
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	36382
Np	0
N optimal	36382
N conservative	36382
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.	220
Corr. Est. Fragment Len.	0.3505
Phantom Peak	55
Corr. Phantom Peak	0.3283
Argmin. Corr.	1500
Min. Corr.	0.1723
NSC	2.0339
RSC	1.1425

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	0.4913

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	0.1656
AUC	0.4953
CHANCE divergence	0.1152
Elbow Point	0.0000
JS Distance	0.8890
Synthetic AUC	0.5063
Synthetic Elbow Point	0.4818
Synthetic JS Distance	0.5324