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Report generated at 2019-11-03 11:31:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81528852	186476942
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79448768	181693684
Mapped(QC-failed)	0	0
% Mapped	97.4500	97.4300
Paired	81528852	186476942
Paired(QC-failed)	0	0
Read1	40764426	93238471
Read1(QC-failed)	0	0
Read2	40764426	93238471
Read2(QC-failed)	0	0
Properly Paired	78028844	178059283
Properly Paired(QC-failed)	0	0
% Properly Paired	95.7100	95.4900
With itself	78933387	180553291
With itself(QC-failed)	0	0
Singletons	515381	1140393
Singletons(QC-failed)	0	0
% Singleton	0.6300	0.6100
Diff. Chroms	128249	425639
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	35225025	78591287
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3143310	1772322
Paired Opt. Dupes	4210	10324
% Dupes/100	0.0892	0.0226

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35213931	78496784
Distinct Read Pairs	32071649	76728433
One Read Pair	29170625	75011080
Two Read Pairs	2676806	1678659
NRF = Distinct/Total	0.9108	0.9775
PBC1 = OnePair/Distinct	0.9095	0.9776
PBC2 = OnePair/TwoPair	10.8975	44.6851

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	64163430	153637930
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64163430	153637930
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	64163430	153637930
Paired(QC-failed)	0	0
Read1	32081715	76818965
Read1(QC-failed)	0	0
Read2	32081715	76818965
Read2(QC-failed)	0	0
Properly Paired	64163430	153637930
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	64163430	153637930
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	28979
Np	0
N optimal	28979
N conservative	28979
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.	170
Corr. Est. Fragment Len.	0.3088
Phantom Peak	50
Corr. Phantom Peak	0.3006
Argmin. Corr.	1500
Min. Corr.	0.1793
NSC	1.7219
RSC	1.0677

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	0.3953

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	0.1951
AUC	0.4949
CHANCE divergence	0.1159
Elbow Point	0.0000
JS Distance	0.8115
Synthetic AUC	0.4959
Synthetic Elbow Point	0.4126
Synthetic JS Distance	0.4734