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Report generated at 2019-10-12 17:40:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79132188	81954026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71723795	79524456
Mapped(QC-failed)	0	0
% Mapped	90.6400	97.0400
Paired	79132188	81954026
Paired(QC-failed)	0	0
Read1	39566094	40977013
Read1(QC-failed)	0	0
Read2	39566094	40977013
Read2(QC-failed)	0	0
Properly Paired	70878283	77093830
Properly Paired(QC-failed)	0	0
% Properly Paired	89.5700	94.0700
With itself	71424685	79098584
With itself(QC-failed)	0	0
Singletons	299110	425872
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5200
Diff. Chroms	216905	1402744
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	33062960	34184517
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2507621	147561
Paired Opt. Dupes	6126	4430
% Dupes/100	0.0758	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33062582	34160894
Distinct Read Pairs	30554988	34013583
One Read Pair	28293605	33872187
Two Read Pairs	2043035	138075
NRF = Distinct/Total	0.9242	0.9957
PBC1 = OnePair/Distinct	0.9260	0.9958
PBC2 = OnePair/TwoPair	13.8488	245.3173

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	61110678	68073912
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61110678	68073912
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	61110678	68073912
Paired(QC-failed)	0	0
Read1	30555339	34036956
Read1(QC-failed)	0	0
Read2	30555339	34036956
Read2(QC-failed)	0	0
Properly Paired	61110678	68073912
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	61110678	68073912
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	127797
Np	0
N optimal	127797
N conservative	127797
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.	120
Corr. Est. Fragment Len.	0.3225
Phantom Peak	55
Corr. Phantom Peak	0.3005
Argmin. Corr.	1500
Min. Corr.	0.2077
NSC	1.5522
RSC	1.2371

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	0.5413

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	0.1139
AUC	0.4948
CHANCE divergence	0.2255
Elbow Point	0.0000
JS Distance	0.8318
Synthetic AUC	0.4997
Synthetic Elbow Point	0.4607
Synthetic JS Distance	0.5611