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Report generated at 2022-01-13 08:57:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52017062	39854584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49611120	37062784
Mapped(QC-failed)	0	0
% Mapped	95.3700	93.0000
Paired	52017062	39854584
Paired(QC-failed)	0	0
Read1	26008531	19927292
Read1(QC-failed)	0	0
Read2	26008531	19927292
Read2(QC-failed)	0	0
Properly Paired	48197848	33407063
Properly Paired(QC-failed)	0	0
% Properly Paired	92.6600	83.8200
With itself	48888009	35838648
With itself(QC-failed)	0	0
Singletons	723111	1224136
Singletons(QC-failed)	0	0
% Singleton	1.3900	3.0700
Diff. Chroms	509761	1658864
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	21634028	13479178
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	270927	344808
Paired Opt. Dupes	12912	7792
% Dupes/100	0.0125	0.0256

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21632398	13471162
Distinct Read Pairs	21361492	13126691
One Read Pair	21093568	12789814
Two Read Pairs	264986	329426
NRF = Distinct/Total	0.9875	0.9744
PBC1 = OnePair/Distinct	0.9875	0.9743
PBC2 = OnePair/TwoPair	79.6026	38.8245

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	42726202	26268740
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42726202	26268740
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42726202	26268740
Paired(QC-failed)	0	0
Read1	21363101	13134370
Read1(QC-failed)	0	0
Read2	21363101	13134370
Read2(QC-failed)	0	0
Properly Paired	42726202	26268740
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42726202	26268740
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	138700
Np	0
N optimal	138700
N conservative	138700
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.	255
Corr. Est. Fragment Len.	0.1960
Phantom Peak	50
Corr. Phantom Peak	0.1926
Argmin. Corr.	1500
Min. Corr.	0.1778
NSC	1.1023
RSC	1.2318

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	0.3226

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	0.1551
AUC	0.4937
CHANCE divergence	0.2480
Elbow Point	0.0000
JS Distance	0.7314
Synthetic AUC	0.5012
Synthetic Elbow Point	0.1753
Synthetic JS Distance	0.4406