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Report generated at 2021-03-18 21:46:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129167464	107748822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127982132	105210529
Mapped(QC-failed)	0	0
% Mapped	99.0800	97.6400
Paired	129167464	107748822
Paired(QC-failed)	0	0
Read1	64583732	53874411
Read1(QC-failed)	0	0
Read2	64583732	53874411
Read2(QC-failed)	0	0
Properly Paired	115391505	89353817
Properly Paired(QC-failed)	0	0
% Properly Paired	89.3300	82.9300
With itself	127425654	104162194
With itself(QC-failed)	0	0
Singletons	556478	1048335
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.9700
Diff. Chroms	6300419	11301530
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	52482186	39900791
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	634252	469856
Paired Opt. Dupes	2976	1823
% Dupes/100	0.0121	0.0118

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52477316	39896493
Distinct Read Pairs	51843273	39426880
One Read Pair	51228751	38982156
Two Read Pairs	598868	431298
NRF = Distinct/Total	0.9879	0.9882
PBC1 = OnePair/Distinct	0.9881	0.9887
PBC2 = OnePair/TwoPair	85.5426	90.3833

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	103695868	78861870
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103695868	78861870
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103695868	78861870
Paired(QC-failed)	0	0
Read1	51847934	39430935
Read1(QC-failed)	0	0
Read2	51847934	39430935
Read2(QC-failed)	0	0
Properly Paired	103695868	78861870
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103695868	78861870
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	205884
Np	0
N optimal	205884
N conservative	205884
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.	0.1767
Phantom Peak	55
Corr. Phantom Peak	0.1746
Argmin. Corr.	1500
Min. Corr.	0.1706
NSC	1.0361
RSC	1.5359

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	0.1591

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	0.2436
AUC	0.4960
CHANCE divergence	0.1407
Elbow Point	0.0000
JS Distance	0.5941
Synthetic AUC	0.5064
Synthetic Elbow Point	0.1466
Synthetic JS Distance	0.3282