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Report generated at 2020-12-04 05:14:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65285866	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63670136	187969057
Mapped(QC-failed)	0	0
% Mapped	97.5300	97.0900
Paired	65285866	193594802
Paired(QC-failed)	0	0
Read1	32642933	96797401
Read1(QC-failed)	0	0
Read2	32642933	96797401
Read2(QC-failed)	0	0
Properly Paired	63270233	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	96.9100	95.1900
With itself	63461914	185784698
With itself(QC-failed)	0	0
Singletons	208222	2184359
Singletons(QC-failed)	0	0
% Singleton	0.3200	1.1300
Diff. Chroms	64782	610670
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	28703737	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	858692	539110
Paired Opt. Dupes	12418	19807
% Dupes/100	0.0299	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28612687	77646644
Distinct Read Pairs	27758475	77172156
One Read Pair	26927954	76701136
Two Read Pairs	807477	467668
NRF = Distinct/Total	0.9701	0.9939
PBC1 = OnePair/Distinct	0.9701	0.9939
PBC2 = OnePair/TwoPair	33.3483	164.0077

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	55690090	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55690090	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55690090	155345422
Paired(QC-failed)	0	0
Read1	27845045	77672711
Read1(QC-failed)	0	0
Read2	27845045	77672711
Read2(QC-failed)	0	0
Properly Paired	55690090	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55690090	155345422
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	93617
Np	0
N optimal	93617
N conservative	93617
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.	220
Corr. Est. Fragment Len.	0.2000
Phantom Peak	50
Corr. Phantom Peak	0.1991
Argmin. Corr.	1500
Min. Corr.	0.1753
NSC	1.1405
RSC	1.0370

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	0.2775

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	0.2250
AUC	0.4945
CHANCE divergence	0.1211
Elbow Point	0.0000
JS Distance	0.6941
Synthetic AUC	0.5033
Synthetic Elbow Point	0.2673
Synthetic JS Distance	0.3743