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Report generated at 2021-02-05 18:14:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97062652	110664060
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95713796	108798311
Mapped(QC-failed)	0	0
% Mapped	98.6100	98.3100
Paired	97062652	110664060
Paired(QC-failed)	0	0
Read1	48531326	55332030
Read1(QC-failed)	0	0
Read2	48531326	55332030
Read2(QC-failed)	0	0
Properly Paired	94645469	106498695
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5100	96.2400
With itself	95189780	108092733
With itself(QC-failed)	0	0
Singletons	524016	705578
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.6400
Diff. Chroms	81556	137878
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	40517435	46232784
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	370587	376972
Paired Opt. Dupes	67781	91434
% Dupes/100	0.0091	0.0082

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40395840	46175998
Distinct Read Pairs	40045628	45807818
One Read Pair	39700888	45456138
Two Read Pairs	340700	344865
NRF = Distinct/Total	0.9913	0.9920
PBC1 = OnePair/Distinct	0.9914	0.9923
PBC2 = OnePair/TwoPair	116.5274	131.8085

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	80293696	91711624
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80293696	91711624
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80293696	91711624
Paired(QC-failed)	0	0
Read1	40146848	45855812
Read1(QC-failed)	0	0
Read2	40146848	45855812
Read2(QC-failed)	0	0
Properly Paired	80293696	91711624
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80293696	91711624
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	79355
Np	0
N optimal	79355
N conservative	79355
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.	0.1742
Phantom Peak	50
Corr. Phantom Peak	0.1831
Argmin. Corr.	1500
Min. Corr.	0.1687
NSC	1.0326
RSC	0.3828

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	0.0370

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	0.3138
AUC	0.4953
CHANCE divergence	0.1021
Elbow Point	0.0000
JS Distance	0.5383
Synthetic AUC	0.5037
Synthetic Elbow Point	0.0291
Synthetic JS Distance	0.2231