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Report generated at 2021-10-23 05:30:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	173377346	186874232
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	171156363	183817074
Mapped(QC-failed)	0	0
% Mapped	98.7200	98.3600
Paired	173377346	186874232
Paired(QC-failed)	0	0
Read1	86688673	93437116
Read1(QC-failed)	0	0
Read2	86688673	93437116
Read2(QC-failed)	0	0
Properly Paired	170230763	181190078
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1900	96.9600
With itself	170598414	182989360
With itself(QC-failed)	0	0
Singletons	557949	827714
Singletons(QC-failed)	0	0
% Singleton	0.3200	0.4400
Diff. Chroms	156749	1011019
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	78355920	79420006
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11983265	3323828
Paired Opt. Dupes	33844	42686
% Dupes/100	0.1529	0.0419

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	78354872	79383916
Distinct Read Pairs	66371755	76061755
One Read Pair	55938697	72820637
Two Read Pairs	9061399	3164810
NRF = Distinct/Total	0.8471	0.9582
PBC1 = OnePair/Distinct	0.8428	0.9574
PBC2 = OnePair/TwoPair	6.1733	23.0095

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	132745310	152192356
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132745310	152192356
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	132745310	152192356
Paired(QC-failed)	0	0
Read1	66372655	76096178
Read1(QC-failed)	0	0
Read2	66372655	76096178
Read2(QC-failed)	0	0
Properly Paired	132745310	152192356
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	132745310	152192356
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	42022
Np	0
N optimal	42022
N conservative	42022
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.	230
Corr. Est. Fragment Len.	0.5116
Phantom Peak	55
Corr. Phantom Peak	0.4582
Argmin. Corr.	1500
Min. Corr.	0.2166
NSC	2.3619
RSC	1.2209

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	0.7950

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	0.0594
AUC	0.4965
CHANCE divergence	0.1492
Elbow Point	0.0000
JS Distance	0.9572
Synthetic AUC	0.4993
Synthetic Elbow Point	0.7098
Synthetic JS Distance	0.7481