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Report generated at 2019-10-31 00:53:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	126448718	186328420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115291038	182595069
Mapped(QC-failed)	0	0
% Mapped	91.1800	98.0000
Paired	126448718	186328420
Paired(QC-failed)	0	0
Read1	63224359	93164210
Read1(QC-failed)	0	0
Read2	63224359	93164210
Read2(QC-failed)	0	0
Properly Paired	111139463	174653171
Properly Paired(QC-failed)	0	0
% Properly Paired	87.8900	93.7300
With itself	112654790	180890277
With itself(QC-failed)	0	0
Singletons	2636248	1704792
Singletons(QC-failed)	0	0
% Singleton	2.0800	0.9100
Diff. Chroms	880820	4529429
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	46423773	73010674
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10954129	6709019
Paired Opt. Dupes	10584	13379
% Dupes/100	0.2360	0.0919

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46423254	72957325
Distinct Read Pairs	35469231	66253408
One Read Pair	26758619	60053338
Two Read Pairs	6879245	5734419
NRF = Distinct/Total	0.7640	0.9081
PBC1 = OnePair/Distinct	0.7544	0.9064
PBC2 = OnePair/TwoPair	3.8898	10.4724

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	70939288	132603310
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70939288	132603310
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70939288	132603310
Paired(QC-failed)	0	0
Read1	35469644	66301655
Read1(QC-failed)	0	0
Read2	35469644	66301655
Read2(QC-failed)	0	0
Properly Paired	70939288	132603310
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70939288	132603310
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	142717
Np	0
N optimal	142717
N conservative	142717
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.	195
Corr. Est. Fragment Len.	0.1787
Phantom Peak	50
Corr. Phantom Peak	0.1796
Argmin. Corr.	1500
Min. Corr.	0.1746
NSC	1.0237
RSC	0.8262

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	0.4972

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	0.1603
AUC	0.4941
CHANCE divergence	0.1634
Elbow Point	0.0000
JS Distance	0.7613
Synthetic AUC	0.5024
Synthetic Elbow Point	0.3695
Synthetic JS Distance	0.4649