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Report generated at 2020-06-06 08:47:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	124963104	126037706
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	122001465	123979523
Mapped(QC-failed)	0	0
% Mapped	97.6300	98.3700
Paired	124963104	126037706
Paired(QC-failed)	0	0
Read1	62481552	63018853
Read1(QC-failed)	0	0
Read2	62481552	63018853
Read2(QC-failed)	0	0
Properly Paired	121009761	122677160
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8400	97.3300
With itself	121538276	123316204
With itself(QC-failed)	0	0
Singletons	463189	663319
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.5300
Diff. Chroms	109130	230443
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	53567251	53582779
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4718530	584944
Paired Opt. Dupes	31393	12360
% Dupes/100	0.0881	0.0109

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53566041	53540225
Distinct Read Pairs	48847596	52956309
One Read Pair	44507115	52397141
Two Read Pairs	4001677	546325
NRF = Distinct/Total	0.9119	0.9891
PBC1 = OnePair/Distinct	0.9111	0.9894
PBC2 = OnePair/TwoPair	11.1221	95.9084

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	97697442	105995670
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97697442	105995670
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97697442	105995670
Paired(QC-failed)	0	0
Read1	48848721	52997835
Read1(QC-failed)	0	0
Read2	48848721	52997835
Read2(QC-failed)	0	0
Properly Paired	97697442	105995670
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97697442	105995670
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	46532
Np	0
N optimal	46532
N conservative	46532
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.	140
Corr. Est. Fragment Len.	0.1729
Phantom Peak	50
Corr. Phantom Peak	0.1842
Argmin. Corr.	1500
Min. Corr.	0.1680
NSC	1.0286
RSC	0.2976

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	0.0368

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	0.2978
AUC	0.4959
CHANCE divergence	0.1157
Elbow Point	0.0000
JS Distance	0.5280
Synthetic AUC	0.4978
Synthetic Elbow Point	0.0833
Synthetic JS Distance	0.2490