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Report generated at 2020-05-22 14:00:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	38581918	122032658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	34239380	118962872
Mapped(QC-failed)	0	0
% Mapped	88.7400	97.4800
Paired	38581918	122032658
Paired(QC-failed)	0	0
Read1	19290959	61016329
Read1(QC-failed)	0	0
Read2	19290959	61016329
Read2(QC-failed)	0	0
Properly Paired	33143429	114858760
Properly Paired(QC-failed)	0	0
% Properly Paired	85.9000	94.1200
With itself	33564773	117388354
With itself(QC-failed)	0	0
Singletons	674607	1574518
Singletons(QC-failed)	0	0
% Singleton	1.7500	1.2900
Diff. Chroms	251072	1710423
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	14761381	49902005
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	228261	628189
Paired Opt. Dupes	3398	7684
% Dupes/100	0.0155	0.0126

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	14760736	49898886
Distinct Read Pairs	14532488	49270740
One Read Pair	14307047	48649123
Two Read Pairs	222682	615143
NRF = Distinct/Total	0.9845	0.9874
PBC1 = OnePair/Distinct	0.9845	0.9874
PBC2 = OnePair/TwoPair	64.2488	79.0859

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	29066240	98547632
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	29066240	98547632
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	29066240	98547632
Paired(QC-failed)	0	0
Read1	14533120	49273816
Read1(QC-failed)	0	0
Read2	14533120	49273816
Read2(QC-failed)	0	0
Properly Paired	29066240	98547632
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	29066240	98547632
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	50644
Np	0
N optimal	50644
N conservative	50644
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.	295
Corr. Est. Fragment Len.	0.2045
Phantom Peak	50
Corr. Phantom Peak	0.1959
Argmin. Corr.	1500
Min. Corr.	0.1786
NSC	1.1451
RSC	1.5013

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	0.1976

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	0.1345
AUC	0.4924
CHANCE divergence	0.4487
Elbow Point	0.0000
JS Distance	0.6803
Synthetic AUC	0.4942
Synthetic Elbow Point	0.1635
Synthetic JS Distance	0.3820