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Report generated at 2020-07-14 10:59:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	68566108	53978528
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63880157	49170794
Mapped(QC-failed)	0	0
% Mapped	93.1700	91.0900
Paired	68566108	53978528
Paired(QC-failed)	0	0
Read1	34283054	26989264
Read1(QC-failed)	0	0
Read2	34283054	26989264
Read2(QC-failed)	0	0
Properly Paired	61010878	47390120
Properly Paired(QC-failed)	0	0
% Properly Paired	88.9800	87.7900
With itself	62874124	48351210
With itself(QC-failed)	0	0
Singletons	1006033	819584
Singletons(QC-failed)	0	0
% Singleton	1.4700	1.5200
Diff. Chroms	1325830	552130
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	26417858	19556389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	337550	746028
Paired Opt. Dupes	2802	2627
% Dupes/100	0.0128	0.0381

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26417754	19556328
Distinct Read Pairs	26080204	18810303
One Read Pair	25746298	18088069
Two Read Pairs	330299	699092
NRF = Distinct/Total	0.9872	0.9619
PBC1 = OnePair/Distinct	0.9872	0.9616
PBC2 = OnePair/TwoPair	77.9485	25.8737

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	52160616	37620722
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52160616	37620722
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52160616	37620722
Paired(QC-failed)	0	0
Read1	26080308	18810361
Read1(QC-failed)	0	0
Read2	26080308	18810361
Read2(QC-failed)	0	0
Properly Paired	52160616	37620722
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52160616	37620722
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	198632
Np	0
N optimal	198632
N conservative	198632
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.	250
Corr. Est. Fragment Len.	0.2132
Phantom Peak	50
Corr. Phantom Peak	0.1983
Argmin. Corr.	1500
Min. Corr.	0.1847
NSC	1.1544
RSC	2.0977

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	0.2714

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	0.1025
AUC	0.4943
CHANCE divergence	0.5035
Elbow Point	0.0000
JS Distance	0.7478
Synthetic AUC	0.5073
Synthetic Elbow Point	0.0579
Synthetic JS Distance	0.4464