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Report generated at 2019-10-13 00:20:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	79893792	109206430
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75616424	106664791
Mapped(QC-failed)	0	0
% Mapped	94.6500	97.6700
Paired	79893792	109206430
Paired(QC-failed)	0	0
Read1	39946896	54603215
Read1(QC-failed)	0	0
Read2	39946896	54603215
Read2(QC-failed)	0	0
Properly Paired	74239054	104044796
Properly Paired(QC-failed)	0	0
% Properly Paired	92.9200	95.2700
With itself	74695658	105477300
With itself(QC-failed)	0	0
Singletons	920766	1187491
Singletons(QC-failed)	0	0
% Singleton	1.1500	1.0900
Diff. Chroms	258576	959464
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	33443722	46114687
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7316705	441722
Paired Opt. Dupes	16706	6992
% Dupes/100	0.2188	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33441514	46055208
Distinct Read Pairs	26125276	45615199
One Read Pair	20230453	45182227
Two Read Pairs	4724047	427658
NRF = Distinct/Total	0.7812	0.9904
PBC1 = OnePair/Distinct	0.7744	0.9905
PBC2 = OnePair/TwoPair	4.2824	105.6504

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	52254034	91345930
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52254034	91345930
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52254034	91345930
Paired(QC-failed)	0	0
Read1	26127017	45672965
Read1(QC-failed)	0	0
Read2	26127017	45672965
Read2(QC-failed)	0	0
Properly Paired	52254034	91345930
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52254034	91345930
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	66118
Np	0
N optimal	66118
N conservative	66118
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.	160
Corr. Est. Fragment Len.	0.1900
Phantom Peak	50
Corr. Phantom Peak	0.1868
Argmin. Corr.	1500
Min. Corr.	0.1616
NSC	1.1754
RSC	1.1266

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	0.2312

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	0.2306
AUC	0.4944
CHANCE divergence	0.1265
Elbow Point	0.0000
JS Distance	0.6873
Synthetic AUC	0.5055
Synthetic Elbow Point	0.2462
Synthetic JS Distance	0.3675