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Report generated at 2019-10-31 04:18:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	132223024	194901230
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	129389313	192136328
Mapped(QC-failed)	0	0
% Mapped	97.8600	98.5800
Paired	132223024	194901230
Paired(QC-failed)	0	0
Read1	66111512	97450615
Read1(QC-failed)	0	0
Read2	66111512	97450615
Read2(QC-failed)	0	0
Properly Paired	126781373	187452194
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8800	96.1800
With itself	128700180	191119169
With itself(QC-failed)	0	0
Singletons	689133	1017159
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5200
Diff. Chroms	1205774	2127070
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	53093233	77977039
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1395188	1865117
Paired Opt. Dupes	15948	13406
% Dupes/100	0.0263	0.0239

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53093025	77969017
Distinct Read Pairs	51697845	76104111
One Read Pair	50331961	74277183
Two Read Pairs	1337181	1790747
NRF = Distinct/Total	0.9737	0.9761
PBC1 = OnePair/Distinct	0.9736	0.9760
PBC2 = OnePair/TwoPair	37.6403	41.4783

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	103396090	152223844
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103396090	152223844
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103396090	152223844
Paired(QC-failed)	0	0
Read1	51698045	76111922
Read1(QC-failed)	0	0
Read2	51698045	76111922
Read2(QC-failed)	0	0
Properly Paired	103396090	152223844
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103396090	152223844
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	155352
Np	0
N optimal	155352
N conservative	155352
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.	140
Corr. Est. Fragment Len.	0.1881
Phantom Peak	50
Corr. Phantom Peak	0.1967
Argmin. Corr.	1500
Min. Corr.	0.1832
NSC	1.0267
RSC	0.3633

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	0.1983

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	0.2430
AUC	0.4952
CHANCE divergence	0.1224
Elbow Point	0.0000
JS Distance	0.6162
Synthetic AUC	0.5028
Synthetic Elbow Point	0.1984
Synthetic JS Distance	0.3362