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Report generated at 2020-05-14 13:18:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	80859852	152308104
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	74636604	148017607
Mapped(QC-failed)	0	0
% Mapped	92.3000	97.1800
Paired	80859852	152308104
Paired(QC-failed)	0	0
Read1	40429926	76154052
Read1(QC-failed)	0	0
Read2	40429926	76154052
Read2(QC-failed)	0	0
Properly Paired	73488468	145664311
Properly Paired(QC-failed)	0	0
% Properly Paired	90.8800	95.6400
With itself	74145026	147236867
With itself(QC-failed)	0	0
Singletons	491578	780740
Singletons(QC-failed)	0	0
% Singleton	0.6100	0.5100
Diff. Chroms	354809	863963
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	32494130	63227368
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	137670	220283
Paired Opt. Dupes	1118	1066
% Dupes/100	0.0042	0.0035

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32489393	63148791
Distinct Read Pairs	32351751	62930074
One Read Pair	32214614	62712523
Two Read Pairs	136634	216455
NRF = Distinct/Total	0.9958	0.9965
PBC1 = OnePair/Distinct	0.9958	0.9965
PBC2 = OnePair/TwoPair	235.7730	289.7255

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	64712920	126014170
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64712920	126014170
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64712920	126014170
Paired(QC-failed)	0	0
Read1	32356460	63007085
Read1(QC-failed)	0	0
Read2	32356460	63007085
Read2(QC-failed)	0	0
Properly Paired	64712920	126014170
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64712920	126014170
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	202358
Np	0
N optimal	202358
N conservative	202358
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.	145
Corr. Est. Fragment Len.	0.1936
Phantom Peak	50
Corr. Phantom Peak	0.2077
Argmin. Corr.	1500
Min. Corr.	0.1842
NSC	1.0509
RSC	0.3994

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	0.3397

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	0.2055
AUC	0.4949
CHANCE divergence	0.1271
Elbow Point	0.0000
JS Distance	0.7143
Synthetic AUC	0.5019
Synthetic Elbow Point	0.2474
Synthetic JS Distance	0.3963