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Report generated at 2022-01-13 04:52:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	42911408	52208364
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	36768380	46961269
Mapped(QC-failed)	0	0
% Mapped	85.6800	89.9500
Paired	42911408	52208364
Paired(QC-failed)	0	0
Read1	21455704	26104182
Read1(QC-failed)	0	0
Read2	21455704	26104182
Read2(QC-failed)	0	0
Properly Paired	35692896	38339710
Properly Paired(QC-failed)	0	0
% Properly Paired	83.1800	73.4400
With itself	36023650	44775897
With itself(QC-failed)	0	0
Singletons	744730	2185372
Singletons(QC-failed)	0	0
% Singleton	1.7400	4.1900
Diff. Chroms	213829	4612399
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	15994491	13624196
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	297408	312822
Paired Opt. Dupes	4052	3040
% Dupes/100	0.0186	0.0230

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15990621	13619156
Distinct Read Pairs	15693287	13306524
One Read Pair	15400720	13000280
Two Read Pairs	287857	300008
NRF = Distinct/Total	0.9814	0.9770
PBC1 = OnePair/Distinct	0.9814	0.9770
PBC2 = OnePair/TwoPair	53.5013	43.3331

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	31394166	26622748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	31394166	26622748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	31394166	26622748
Paired(QC-failed)	0	0
Read1	15697083	13311374
Read1(QC-failed)	0	0
Read2	15697083	13311374
Read2(QC-failed)	0	0
Properly Paired	31394166	26622748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	31394166	26622748
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	56779
Np	0
N optimal	56779
N conservative	56779
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.	290
Corr. Est. Fragment Len.	0.2520
Phantom Peak	50
Corr. Phantom Peak	0.2326
Argmin. Corr.	1500
Min. Corr.	0.1885
NSC	1.3368
RSC	1.4387

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	0.3756

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	0.1421
AUC	0.4927
CHANCE divergence	0.2670
Elbow Point	0.0000
JS Distance	0.7549
Synthetic AUC	0.5021
Synthetic Elbow Point	0.2752
Synthetic JS Distance	0.4761