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Report generated at 2019-11-03 16:50:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	158608548	158940554
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	157277305	157152767
Mapped(QC-failed)	0	0
% Mapped	99.1600	98.8800
Paired	158608548	158940554
Paired(QC-failed)	0	0
Read1	79304274	79470277
Read1(QC-failed)	0	0
Read2	79304274	79470277
Read2(QC-failed)	0	0
Properly Paired	155341394	154442853
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9400	97.1700
With itself	156708068	156399332
With itself(QC-failed)	0	0
Singletons	569237	753435
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.4700
Diff. Chroms	837408	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	70483556	68222921
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7918133	2746068
Paired Opt. Dupes	28566	28097
% Dupes/100	0.1123	0.0403

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	70460085	68139154
Distinct Read Pairs	62544589	65397649
One Read Pair	55372925	62741963
Two Read Pairs	6489036	2573454
NRF = Distinct/Total	0.8877	0.9598
PBC1 = OnePair/Distinct	0.8853	0.9594
PBC2 = OnePair/TwoPair	8.5333	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	125130846	130953706
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125130846	130953706
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	125130846	130953706
Paired(QC-failed)	0	0
Read1	62565423	65476853
Read1(QC-failed)	0	0
Read2	62565423	65476853
Read2(QC-failed)	0	0
Properly Paired	125130846	130953706
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	125130846	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	139810
Np	0
N optimal	139810
N conservative	139810
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.	165
Corr. Est. Fragment Len.	0.1905
Phantom Peak	50
Corr. Phantom Peak	0.1945
Argmin. Corr.	1500
Min. Corr.	0.1779
NSC	1.0709
RSC	0.7586

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	0.4859

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	0.1963
AUC	0.4964
CHANCE divergence	0.1035
Elbow Point	0.0000
JS Distance	0.8192
Synthetic AUC	0.5004
Synthetic Elbow Point	0.3550
Synthetic JS Distance	0.4384