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Report generated at 2022-01-14 03:13:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	30566918	73857574
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	23380042	71880916
Mapped(QC-failed)	0	0
% Mapped	76.4900	97.3200
Paired	30566918	73857574
Paired(QC-failed)	0	0
Read1	15283459	36928787
Read1(QC-failed)	0	0
Read2	15283459	36928787
Read2(QC-failed)	0	0
Properly Paired	22451719	56693280
Properly Paired(QC-failed)	0	0
% Properly Paired	73.4500	76.7600
With itself	23115389	70763351
With itself(QC-failed)	0	0
Singletons	264653	1117565
Singletons(QC-failed)	0	0
% Singleton	0.8700	1.5100
Diff. Chroms	90009	11478644
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	10113157	24996827
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2760253	241052
Paired Opt. Dupes	955	1015
% Dupes/100	0.2729	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	10109352	24993555
Distinct Read Pairs	7350093	24752593
One Read Pair	5212858	24516128
Two Read Pairs	1638289	233547
NRF = Distinct/Total	0.7271	0.9904
PBC1 = OnePair/Distinct	0.7092	0.9904
PBC2 = OnePair/TwoPair	3.1819	104.9730

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	14705808	49511550
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	14705808	49511550
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	14705808	49511550
Paired(QC-failed)	0	0
Read1	7352904	24755775
Read1(QC-failed)	0	0
Read2	7352904	24755775
Read2(QC-failed)	0	0
Properly Paired	14705808	49511550
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	14705808	49511550
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	60959
Np	0
N optimal	60959
N conservative	60959
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 (11M)

	rep1
Reads	11827824
Est. Fragment Len.	145
Corr. Est. Fragment Len.	0.1341
Phantom Peak	50
Corr. Phantom Peak	0.1148
Argmin. Corr.	1500
Min. Corr.	0.1038
NSC	1.2919
RSC	2.7665

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	0.1420

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	0.1932
AUC	0.4894
CHANCE divergence	0.3343
Elbow Point	0.0000
JS Distance	0.6629
Synthetic AUC	0.5067
Synthetic Elbow Point	0.1704
Synthetic JS Distance	0.3133