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Report generated at 2022-01-08 05:54:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	133442954	130176754
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	131050769	124658283
Mapped(QC-failed)	0	0
% Mapped	98.2100	95.7600
Paired	133442954	130176754
Paired(QC-failed)	0	0
Read1	66721477	65088377
Read1(QC-failed)	0	0
Read2	66721477	65088377
Read2(QC-failed)	0	0
Properly Paired	112892164	102167555
Properly Paired(QC-failed)	0	0
% Properly Paired	84.6000	78.4800
With itself	129840848	122523087
With itself(QC-failed)	0	0
Singletons	1209921	2135196
Singletons(QC-failed)	0	0
% Singleton	0.9100	1.6400
Diff. Chroms	8753863	14641335
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	50997385	44771849
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2772661	568051
Paired Opt. Dupes	669	648
% Dupes/100	0.0544	0.0127

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50979157	44746969
Distinct Read Pairs	48209145	44182877
One Read Pair	45581293	43638722
Two Read Pairs	2495403	533088
NRF = Distinct/Total	0.9457	0.9874
PBC1 = OnePair/Distinct	0.9455	0.9877
PBC2 = OnePair/TwoPair	18.2661	81.8603

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	96449448	88407596
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96449448	88407596
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	96449448	88407596
Paired(QC-failed)	0	0
Read1	48224724	44203798
Read1(QC-failed)	0	0
Read2	48224724	44203798
Read2(QC-failed)	0	0
Properly Paired	96449448	88407596
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	96449448	88407596
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	208955
Np	0
N optimal	208955
N conservative	208955
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.	0.1768
Phantom Peak	55
Corr. Phantom Peak	0.1735
Argmin. Corr.	1500
Min. Corr.	0.1696
NSC	1.0426
RSC	1.8575

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	0.2076

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	0.2370
AUC	0.4959
CHANCE divergence	0.1179
Elbow Point	0.0000
JS Distance	0.6345
Synthetic AUC	0.5072
Synthetic Elbow Point	0.1830
Synthetic JS Distance	0.3459