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Report generated at 2022-01-11 08:45:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	71516838	98701132
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70692781	96181840
Mapped(QC-failed)	0	0
% Mapped	98.8500	97.4500
Paired	71516838	98701132
Paired(QC-failed)	0	0
Read1	35758419	49350566
Read1(QC-failed)	0	0
Read2	35758419	49350566
Read2(QC-failed)	0	0
Properly Paired	63983664	77055364
Properly Paired(QC-failed)	0	0
% Properly Paired	89.4700	78.0700
With itself	70199089	94971565
With itself(QC-failed)	0	0
Singletons	493692	1210275
Singletons(QC-failed)	0	0
% Singleton	0.6900	1.2300
Diff. Chroms	5453977	14544721
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	29820598	34047307
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	448856	359515
Paired Opt. Dupes	2630	1894
% Dupes/100	0.0151	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29817201	34044272
Distinct Read Pairs	29368419	33684905
One Read Pair	28930457	33341128
Two Read Pairs	427899	333429
NRF = Distinct/Total	0.9849	0.9894
PBC1 = OnePair/Distinct	0.9851	0.9898
PBC2 = OnePair/TwoPair	67.6105	99.9947

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	58743484	67375584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58743484	67375584
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58743484	67375584
Paired(QC-failed)	0	0
Read1	29371742	33687792
Read1(QC-failed)	0	0
Read2	29371742	33687792
Read2(QC-failed)	0	0
Properly Paired	58743484	67375584
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58743484	67375584
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	166373
Np	0
N optimal	166373
N conservative	166373
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.	0.2012
Phantom Peak	55
Corr. Phantom Peak	0.1891
Argmin. Corr.	1500
Min. Corr.	0.1776
NSC	1.1328
RSC	2.0441

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	0.5702

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	0.1237
AUC	0.4947
CHANCE divergence	0.2243
Elbow Point	0.0000
JS Distance	0.8043
Synthetic AUC	0.5033
Synthetic Elbow Point	0.3587
Synthetic JS Distance	0.5244