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Report generated at 2020-05-28 18:19:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129890152	129938162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129090801	127236885
Mapped(QC-failed)	0	0
% Mapped	99.3800	97.9200
Paired	129890152	129938162
Paired(QC-failed)	0	0
Read1	64945076	64969081
Read1(QC-failed)	0	0
Read2	64945076	64969081
Read2(QC-failed)	0	0
Properly Paired	128446208	124171445
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8900	95.5600
With itself	128635405	126465025
With itself(QC-failed)	0	0
Singletons	455396	771860
Singletons(QC-failed)	0	0
% Singleton	0.3500	0.5900
Diff. Chroms	38973	239141
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	60129334	54765466
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	667619	445838
Paired Opt. Dupes	1752	1418
% Dupes/100	0.0111	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60111826	54644116
Distinct Read Pairs	59445727	54251549
One Read Pair	58791466	53877110
Two Read Pairs	643375	366240
NRF = Distinct/Total	0.9889	0.9928
PBC1 = OnePair/Distinct	0.9890	0.9931
PBC2 = OnePair/TwoPair	91.3798	147.1088

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	118923430	108639256
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118923430	108639256
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	118923430	108639256
Paired(QC-failed)	0	0
Read1	59461715	54319628
Read1(QC-failed)	0	0
Read2	59461715	54319628
Read2(QC-failed)	0	0
Properly Paired	118923430	108639256
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	118923430	108639256
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	260464
Np	0
N optimal	260464
N conservative	260464
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.	0.1873
Phantom Peak	45
Corr. Phantom Peak	0.1842
Argmin. Corr.	1500
Min. Corr.	0.1741
NSC	1.0759
RSC	1.2991

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	0.4226

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	0.1992
AUC	0.4963
CHANCE divergence	0.1144
Elbow Point	0.0000
JS Distance	0.7245
Synthetic AUC	0.5037
Synthetic Elbow Point	0.2454
Synthetic JS Distance	0.4145