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Report generated at 2021-03-20 01:24:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	95760278	140350086
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94515062	136223961
Mapped(QC-failed)	0	0
% Mapped	98.7000	97.0600
Paired	95760278	140350086
Paired(QC-failed)	0	0
Read1	47880139	70175043
Read1(QC-failed)	0	0
Read2	47880139	70175043
Read2(QC-failed)	0	0
Properly Paired	87275130	120532551
Properly Paired(QC-failed)	0	0
% Properly Paired	91.1400	85.8800
With itself	93843651	134681268
With itself(QC-failed)	0	0
Singletons	671411	1542693
Singletons(QC-failed)	0	0
% Singleton	0.7000	1.1000
Diff. Chroms	5157684	9773665
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	40637644	53789939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	490880	594512
Paired Opt. Dupes	2015	1824
% Dupes/100	0.0121	0.0111

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40634269	53785343
Distinct Read Pairs	40143476	53191094
One Read Pair	39668169	52633239
Two Read Pairs	462089	539980
NRF = Distinct/Total	0.9879	0.9890
PBC1 = OnePair/Distinct	0.9882	0.9895
PBC2 = OnePair/TwoPair	85.8453	97.4726

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	80293528	106390854
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80293528	106390854
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80293528	106390854
Paired(QC-failed)	0	0
Read1	40146764	53195427
Read1(QC-failed)	0	0
Read2	40146764	53195427
Read2(QC-failed)	0	0
Properly Paired	80293528	106390854
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80293528	106390854
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	224043
Np	0
N optimal	224043
N conservative	224043
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.	150
Corr. Est. Fragment Len.	0.1873
Phantom Peak	55
Corr. Phantom Peak	0.1807
Argmin. Corr.	1500
Min. Corr.	0.1738
NSC	1.0774
RSC	1.9682

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	0.4688

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	0.1723
AUC	0.4955
CHANCE divergence	0.1436
Elbow Point	0.0000
JS Distance	0.7483
Synthetic AUC	0.4989
Synthetic Elbow Point	0.3079
Synthetic JS Distance	0.4515