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Report generated at 2019-10-13 05:04:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	84162836	106180416
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78175075	98634603
Mapped(QC-failed)	0	0
% Mapped	92.8900	92.8900
Paired	84162836	106180416
Paired(QC-failed)	0	0
Read1	42081418	53090208
Read1(QC-failed)	0	0
Read2	42081418	53090208
Read2(QC-failed)	0	0
Properly Paired	72820223	91384537
Properly Paired(QC-failed)	0	0
% Properly Paired	86.5200	86.0700
With itself	73417512	92607301
With itself(QC-failed)	0	0
Singletons	4757563	6027302
Singletons(QC-failed)	0	0
% Singleton	5.6500	5.6800
Diff. Chroms	300779	792771
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	29501806	37373521
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2670722	355831
Paired Opt. Dupes	2624	3074
% Dupes/100	0.0905	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29500857	37338415
Distinct Read Pairs	26830224	36983246
One Read Pair	24406122	36645916
Two Read Pairs	2200718	328129
NRF = Distinct/Total	0.9095	0.9905
PBC1 = OnePair/Distinct	0.9096	0.9909
PBC2 = OnePair/TwoPair	11.0901	111.6814

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	53662168	74035380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53662168	74035380
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53662168	74035380
Paired(QC-failed)	0	0
Read1	26831084	37017690
Read1(QC-failed)	0	0
Read2	26831084	37017690
Read2(QC-failed)	0	0
Properly Paired	53662168	74035380
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53662168	74035380
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	35668
Np	0
N optimal	35668
N conservative	35668
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.	135
Corr. Est. Fragment Len.	0.1721
Phantom Peak	50
Corr. Phantom Peak	0.1828
Argmin. Corr.	1500
Min. Corr.	0.1658
NSC	1.0377
RSC	0.3673

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	0.0628

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	0.2969
AUC	0.4944
CHANCE divergence	0.1098
Elbow Point	0.0000
JS Distance	0.5522
Synthetic AUC	0.5104
Synthetic Elbow Point	0.0888
Synthetic JS Distance	0.2500