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Report generated at 2020-06-10 18:23:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	86766764	134911976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78508701	131561748
Mapped(QC-failed)	0	0
% Mapped	90.4800	97.5200
Paired	86766764	134911976
Paired(QC-failed)	0	0
Read1	43383382	67455988
Read1(QC-failed)	0	0
Read2	43383382	67455988
Read2(QC-failed)	0	0
Properly Paired	76218200	129326575
Properly Paired(QC-failed)	0	0
% Properly Paired	87.8400	95.8600
With itself	77365129	130892790
With itself(QC-failed)	0	0
Singletons	1143572	668958
Singletons(QC-failed)	0	0
% Singleton	1.3200	0.5000
Diff. Chroms	364771	887686
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	28803302	56597685
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	148090	240684
Paired Opt. Dupes	1174	1949
% Dupes/100	0.0051	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28800275	56554078
Distinct Read Pairs	28652206	56313956
One Read Pair	28505469	56074958
Two Read Pairs	145479	237897
NRF = Distinct/Total	0.9949	0.9958
PBC1 = OnePair/Distinct	0.9949	0.9958
PBC2 = OnePair/TwoPair	195.9422	235.7111

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	57310424	112714002
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57310424	112714002
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	57310424	112714002
Paired(QC-failed)	0	0
Read1	28655212	56357001
Read1(QC-failed)	0	0
Read2	28655212	56357001
Read2(QC-failed)	0	0
Properly Paired	57310424	112714002
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	57310424	112714002
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	140478
Np	0
N optimal	140478
N conservative	140478
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.	135
Corr. Est. Fragment Len.	0.2000
Phantom Peak	50
Corr. Phantom Peak	0.2484
Argmin. Corr.	1500
Min. Corr.	0.1878
NSC	1.0649
RSC	0.2010

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	0.1514

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	0.2525
AUC	0.4946
CHANCE divergence	0.1179
Elbow Point	0.0000
JS Distance	0.6267
Synthetic AUC	0.4997
Synthetic Elbow Point	0.1474
Synthetic JS Distance	0.3177