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Report generated at 2020-07-09 13:41:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	75133308	109897006
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71772985	108231726
Mapped(QC-failed)	0	0
% Mapped	95.5300	98.4800
Paired	75133308	109897006
Paired(QC-failed)	0	0
Read1	37566654	54948503
Read1(QC-failed)	0	0
Read2	37566654	54948503
Read2(QC-failed)	0	0
Properly Paired	71049292	105268015
Properly Paired(QC-failed)	0	0
% Properly Paired	94.5600	95.7900
With itself	71434609	107714777
With itself(QC-failed)	0	0
Singletons	338376	516949
Singletons(QC-failed)	0	0
% Singleton	0.4500	0.4700
Diff. Chroms	26972	292990
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	32680435	46292526
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4977825	315764
Paired Opt. Dupes	2585	2945
% Dupes/100	0.1523	0.0068

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32594239	46198469
Distinct Read Pairs	27637617	45905006
One Read Pair	23485144	45622153
Two Read Pairs	3571242	278233
NRF = Distinct/Total	0.8479	0.9936
PBC1 = OnePair/Distinct	0.8498	0.9938
PBC2 = OnePair/TwoPair	6.5762	163.9710

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	55405220	91953524
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55405220	91953524
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55405220	91953524
Paired(QC-failed)	0	0
Read1	27702610	45976762
Read1(QC-failed)	0	0
Read2	27702610	45976762
Read2(QC-failed)	0	0
Properly Paired	55405220	91953524
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55405220	91953524
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	90213
Np	0
N optimal	90213
N conservative	90213
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.	145
Corr. Est. Fragment Len.	0.2471
Phantom Peak	55
Corr. Phantom Peak	0.1898
Argmin. Corr.	1500
Min. Corr.	0.1493
NSC	1.6548
RSC	2.4136

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	0.4158

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	0.1742
AUC	0.4945
CHANCE divergence	0.1414
Elbow Point	0.0000
JS Distance	0.7936
Synthetic AUC	0.5093
Synthetic Elbow Point	0.3800
Synthetic JS Distance	0.4732