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Report generated at 2019-10-12 23:56:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106077946	87587868
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104454460	85042791
Mapped(QC-failed)	0	0
% Mapped	98.4700	97.0900
Paired	106077946	87587868
Paired(QC-failed)	0	0
Read1	53038973	43793934
Read1(QC-failed)	0	0
Read2	53038973	43793934
Read2(QC-failed)	0	0
Properly Paired	103695833	83193525
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7500	94.9800
With itself	103964613	83956805
With itself(QC-failed)	0	0
Singletons	489847	1085986
Singletons(QC-failed)	0	0
% Singleton	0.4600	1.2400
Diff. Chroms	96949	333038
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	46698160	36699350
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11090873	221028
Paired Opt. Dupes	6229	15561
% Dupes/100	0.2375	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46697603	36659304
Distinct Read Pairs	35606836	36439024
One Read Pair	26929392	36223105
Two Read Pairs	6755509	213134
NRF = Distinct/Total	0.7625	0.9940
PBC1 = OnePair/Distinct	0.7563	0.9941
PBC2 = OnePair/TwoPair	3.9863	169.9546

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	71214574	72956644
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71214574	72956644
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71214574	72956644
Paired(QC-failed)	0	0
Read1	35607287	36478322
Read1(QC-failed)	0	0
Read2	35607287	36478322
Read2(QC-failed)	0	0
Properly Paired	71214574	72956644
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71214574	72956644
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	161083
Np	0
N optimal	161083
N conservative	161083
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.	125
Corr. Est. Fragment Len.	0.1630
Phantom Peak	50
Corr. Phantom Peak	0.1665
Argmin. Corr.	1500
Min. Corr.	0.1591
NSC	1.0240
RSC	0.5189

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	0.1200

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	0.2598
AUC	0.4952
CHANCE divergence	0.1261
Elbow Point	0.0000
JS Distance	0.5956
Synthetic AUC	0.4983
Synthetic Elbow Point	0.1232
Synthetic JS Distance	0.3005