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Report generated at 2021-02-06 01:44:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	123978642	114964496
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122581833	113057292
Mapped(QC-failed)	0	0
% Mapped	98.8700	98.3400
Paired	123978642	114964496
Paired(QC-failed)	0	0
Read1	61989321	57482248
Read1(QC-failed)	0	0
Read2	61989321	57482248
Read2(QC-failed)	0	0
Properly Paired	121225075	110989369
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7800	96.5400
With itself	121982141	112354296
With itself(QC-failed)	0	0
Singletons	599692	702996
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.6100
Diff. Chroms	83403	166080
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	52847667	48236755
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	594824	258071
Paired Opt. Dupes	62938	15943
% Dupes/100	0.0113	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52768190	48217442
Distinct Read Pairs	52181612	47960279
One Read Pair	51604252	47714915
Two Read Pairs	569940	240532
NRF = Distinct/Total	0.9889	0.9947
PBC1 = OnePair/Distinct	0.9889	0.9949
PBC2 = OnePair/TwoPair	90.5433	198.3724

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	104505686	95957368
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104505686	95957368
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	104505686	95957368
Paired(QC-failed)	0	0
Read1	52252843	47978684
Read1(QC-failed)	0	0
Read2	52252843	47978684
Read2(QC-failed)	0	0
Properly Paired	104505686	95957368
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	104505686	95957368
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	148430
Np	0
N optimal	148430
N conservative	148430
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.	0.1732
Phantom Peak	50
Corr. Phantom Peak	0.1767
Argmin. Corr.	1500
Min. Corr.	0.1676
NSC	1.0334
RSC	0.6108

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	0.0780

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	0.3062
AUC	0.4959
CHANCE divergence	0.1004
Elbow Point	0.0000
JS Distance	0.5655
Synthetic AUC	0.5057
Synthetic Elbow Point	0.0420
Synthetic JS Distance	0.2365