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Report generated at 2020-05-03 23:43:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	143412514	176817872
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122595983	173073807
Mapped(QC-failed)	0	0
% Mapped	85.4800	97.8800
Paired	143412514	176817872
Paired(QC-failed)	0	0
Read1	71706257	88408936
Read1(QC-failed)	0	0
Read2	71706257	88408936
Read2(QC-failed)	0	0
Properly Paired	120718912	171003617
Properly Paired(QC-failed)	0	0
% Properly Paired	84.1800	96.7100
With itself	121738710	172265942
With itself(QC-failed)	0	0
Singletons	857273	807865
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.4600
Diff. Chroms	469477	503576
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	54860812	75220911
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	343242	718589
Paired Opt. Dupes	2045	2612
% Dupes/100	0.0063	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54856324	75167057
Distinct Read Pairs	54513126	74449701
One Read Pair	54172178	73740092
Two Read Pairs	338753	702144
NRF = Distinct/Total	0.9937	0.9905
PBC1 = OnePair/Distinct	0.9937	0.9905
PBC2 = OnePair/TwoPair	159.9165	105.0213

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	109035140	149004644
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	109035140	149004644
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	109035140	149004644
Paired(QC-failed)	0	0
Read1	54517570	74502322
Read1(QC-failed)	0	0
Read2	54517570	74502322
Read2(QC-failed)	0	0
Properly Paired	109035140	149004644
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	109035140	149004644
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	222632
Np	0
N optimal	222632
N conservative	222632
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.	130
Corr. Est. Fragment Len.	0.1884
Phantom Peak	50
Corr. Phantom Peak	0.2020
Argmin. Corr.	1500
Min. Corr.	0.1749
NSC	1.0774
RSC	0.4987

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	0.2507

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	0.2043
AUC	0.4961
CHANCE divergence	0.1439
Elbow Point	0.0000
JS Distance	0.6704
Synthetic AUC	0.5066
Synthetic Elbow Point	0.1326
Synthetic JS Distance	0.3952