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Report generated at 2020-05-21 10:52:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	169322156	176817872
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	125870625	173073807
Mapped(QC-failed)	0	0
% Mapped	74.3400	97.8800
Paired	169322156	176817872
Paired(QC-failed)	0	0
Read1	84661078	88408936
Read1(QC-failed)	0	0
Read2	84661078	88408936
Read2(QC-failed)	0	0
Properly Paired	123140704	171003617
Properly Paired(QC-failed)	0	0
% Properly Paired	72.7300	96.7100
With itself	124552329	172265942
With itself(QC-failed)	0	0
Singletons	1318296	807865
Singletons(QC-failed)	0	0
% Singleton	0.7800	0.4600
Diff. Chroms	575334	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	54666701	75220911
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	503073	718589
Paired Opt. Dupes	1815	2612
% Dupes/100	0.0092	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54659667	75167057
Distinct Read Pairs	54156676	74449701
One Read Pair	53659621	73740092
Two Read Pairs	491481	702144
NRF = Distinct/Total	0.9908	0.9905
PBC1 = OnePair/Distinct	0.9908	0.9905
PBC2 = OnePair/TwoPair	109.1794	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	108327256	149004644
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108327256	149004644
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	108327256	149004644
Paired(QC-failed)	0	0
Read1	54163628	74502322
Read1(QC-failed)	0	0
Read2	54163628	74502322
Read2(QC-failed)	0	0
Properly Paired	108327256	149004644
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	108327256	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	249352
Np	0
N optimal	249352
N conservative	249352
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.	115
Corr. Est. Fragment Len.	0.1919
Phantom Peak	50
Corr. Phantom Peak	0.2194
Argmin. Corr.	1500
Min. Corr.	0.1758
NSC	1.0914
RSC	0.3682

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	0.2822

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	0.2016
AUC	0.4961
CHANCE divergence	0.1432
Elbow Point	0.0000
JS Distance	0.6776
Synthetic AUC	0.4992
Synthetic Elbow Point	0.1490
Synthetic JS Distance	0.4015