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Report generated at 2020-05-20 19:34:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	161086910	116197260
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	159115788	114125531
Mapped(QC-failed)	0	0
% Mapped	98.7800	98.2200
Paired	161086910	116197260
Paired(QC-failed)	0	0
Read1	80543455	58098630
Read1(QC-failed)	0	0
Read2	80543455	58098630
Read2(QC-failed)	0	0
Properly Paired	157813605	111936342
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9700	96.3300
With itself	158300635	113460777
With itself(QC-failed)	0	0
Singletons	815153	664754
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.5700
Diff. Chroms	63568	109989
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	68466122	49424273
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3565747	404585
Paired Opt. Dupes	2373	1429
% Dupes/100	0.0521	0.0082

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68462987	49418586
Distinct Read Pairs	64897445	49014360
One Read Pair	61496041	48629916
Two Read Pairs	3247582	376015
NRF = Distinct/Total	0.9479	0.9918
PBC1 = OnePair/Distinct	0.9476	0.9922
PBC2 = OnePair/TwoPair	18.9359	129.3297

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	129800750	98039376
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129800750	98039376
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	129800750	98039376
Paired(QC-failed)	0	0
Read1	64900375	49019688
Read1(QC-failed)	0	0
Read2	64900375	49019688
Read2(QC-failed)	0	0
Properly Paired	129800750	98039376
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	129800750	98039376
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	227988
Np	0
N optimal	227988
N conservative	227988
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.	150
Corr. Est. Fragment Len.	0.1830
Phantom Peak	50
Corr. Phantom Peak	0.1873
Argmin. Corr.	1500
Min. Corr.	0.1757
NSC	1.0420
RSC	0.6317

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	0.1739

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	0.2416
AUC	0.4964
CHANCE divergence	0.1131
Elbow Point	0.0000
JS Distance	0.6033
Synthetic AUC	0.4969
Synthetic Elbow Point	0.1624
Synthetic JS Distance	0.3464