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Report generated at 2019-10-13 04:17:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	123260668	74890440
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	119060921	73000884
Mapped(QC-failed)	0	0
% Mapped	96.5900	97.4800
Paired	123260668	74890440
Paired(QC-failed)	0	0
Read1	61630334	37445220
Read1(QC-failed)	0	0
Read2	61630334	37445220
Read2(QC-failed)	0	0
Properly Paired	117242524	71988853
Properly Paired(QC-failed)	0	0
% Properly Paired	95.1200	96.1300
With itself	117834060	72310070
With itself(QC-failed)	0	0
Singletons	1226861	690814
Singletons(QC-failed)	0	0
% Singleton	1.0000	0.9200
Diff. Chroms	115195	118954
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	49165407	31543148
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4656285	2120305
Paired Opt. Dupes	5381	2379
% Dupes/100	0.0947	0.0672

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49164683	31498588
Distinct Read Pairs	44508458	29382089
One Read Pair	40299025	27417596
Two Read Pairs	3806332	1823795
NRF = Distinct/Total	0.9053	0.9328
PBC1 = OnePair/Distinct	0.9054	0.9331
PBC2 = OnePair/TwoPair	10.5874	15.0333

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	89018244	58845686
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89018244	58845686
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	89018244	58845686
Paired(QC-failed)	0	0
Read1	44509122	29422843
Read1(QC-failed)	0	0
Read2	44509122	29422843
Read2(QC-failed)	0	0
Properly Paired	89018244	58845686
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	89018244	58845686
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	44260
Np	0
N optimal	44260
N conservative	44260
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.	115
Corr. Est. Fragment Len.	0.1803
Phantom Peak	50
Corr. Phantom Peak	0.2049
Argmin. Corr.	1500
Min. Corr.	0.1745
NSC	1.0333
RSC	0.1915

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	0.0184

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	0.3069
AUC	0.4957
CHANCE divergence	0.1044
Elbow Point	0.0000
JS Distance	0.5282
Synthetic AUC	0.5022
Synthetic Elbow Point	0.0393
Synthetic JS Distance	0.2364