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Report generated at 2022-01-13 05:09:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	51439606	39854584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44147970	37062784
Mapped(QC-failed)	0	0
% Mapped	85.8200	93.0000
Paired	51439606	39854584
Paired(QC-failed)	0	0
Read1	25719803	19927292
Read1(QC-failed)	0	0
Read2	25719803	19927292
Read2(QC-failed)	0	0
Properly Paired	42640850	33407063
Properly Paired(QC-failed)	0	0
% Properly Paired	82.8900	83.8200
With itself	43149465	35838648
With itself(QC-failed)	0	0
Singletons	998505	1224136
Singletons(QC-failed)	0	0
% Singleton	1.9400	3.0700
Diff. Chroms	367291	1658864
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	19007771	13479178
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	450667	344808
Paired Opt. Dupes	10305	7792
% Dupes/100	0.0237	0.0256

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19004640	13471162
Distinct Read Pairs	18554045	13126691
One Read Pair	18112918	12789814
Two Read Pairs	431874	329426
NRF = Distinct/Total	0.9763	0.9744
PBC1 = OnePair/Distinct	0.9762	0.9743
PBC2 = OnePair/TwoPair	41.9403	38.8245

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	37114208	26268740
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37114208	26268740
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	37114208	26268740
Paired(QC-failed)	0	0
Read1	18557104	13134370
Read1(QC-failed)	0	0
Read2	18557104	13134370
Read2(QC-failed)	0	0
Properly Paired	37114208	26268740
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	37114208	26268740
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	28223
Np	0
N optimal	28223
N conservative	28223
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.	285
Corr. Est. Fragment Len.	0.4561
Phantom Peak	55
Corr. Phantom Peak	0.3887
Argmin. Corr.	1500
Min. Corr.	0.2069
NSC	2.2042
RSC	1.3705

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	0.6717

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	0.0616
AUC	0.4932
CHANCE divergence	0.4033
Elbow Point	0.0000
JS Distance	0.9055
Synthetic AUC	0.5014
Synthetic Elbow Point	0.5500
Synthetic JS Distance	0.6651