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Report generated at 2021-02-05 11:30:21

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	56638396	114808036
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54162572	112966653
Mapped(QC-failed)	0	0
% Mapped	95.6300	98.4000
Paired	56638396	114808036
Paired(QC-failed)	0	0
Read1	28319198	57404018
Read1(QC-failed)	0	0
Read2	28319198	57404018
Read2(QC-failed)	0	0
Properly Paired	53239242	111166608
Properly Paired(QC-failed)	0	0
% Properly Paired	94.0000	96.8300
With itself	53878105	112278723
With itself(QC-failed)	0	0
Singletons	284467	687930
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.6000
Diff. Chroms	32595	128846
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	24108809	48311888
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3226310	307480
Paired Opt. Dupes	35480	76418
% Dupes/100	0.1338	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24101893	48289765
Distinct Read Pairs	20876508	47983591
One Read Pair	18024491	47690244
Two Read Pairs	2524260	287957
NRF = Distinct/Total	0.8662	0.9937
PBC1 = OnePair/Distinct	0.8634	0.9939
PBC2 = OnePair/TwoPair	7.1405	165.6159

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	41764998	96008816
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	41764998	96008816
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	41764998	96008816
Paired(QC-failed)	0	0
Read1	20882499	48004408
Read1(QC-failed)	0	0
Read2	20882499	48004408
Read2(QC-failed)	0	0
Properly Paired	41764998	96008816
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	41764998	96008816
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	83118
Np	0
N optimal	83118
N conservative	83118
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.	145
Corr. Est. Fragment Len.	0.1898
Phantom Peak	55
Corr. Phantom Peak	0.1665
Argmin. Corr.	1500
Min. Corr.	0.1508
NSC	1.2584
RSC	2.4931

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	0.1822

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	0.2428
AUC	0.4935
CHANCE divergence	0.1389
Elbow Point	0.0000
JS Distance	0.6409
Synthetic AUC	0.5033
Synthetic Elbow Point	0.1888
Synthetic JS Distance	0.3343