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Report generated at 2019-10-13 04:47:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98931668	84831728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95226332	78378634
Mapped(QC-failed)	0	0
% Mapped	96.2500	92.3900
Paired	98931668	84831728
Paired(QC-failed)	0	0
Read1	49465834	42415864
Read1(QC-failed)	0	0
Read2	49465834	42415864
Read2(QC-failed)	0	0
Properly Paired	93720488	77370313
Properly Paired(QC-failed)	0	0
% Properly Paired	94.7300	91.2000
With itself	94782481	78051674
With itself(QC-failed)	0	0
Singletons	443851	326960
Singletons(QC-failed)	0	0
% Singleton	0.4500	0.3900
Diff. Chroms	93745	132697
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	40399618	34106970
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4974149	361659
Paired Opt. Dupes	2647	2500
% Dupes/100	0.1231	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40397925	33930415
Distinct Read Pairs	35423998	33579942
One Read Pair	30966629	33235626
Two Read Pairs	3988824	339365
NRF = Distinct/Total	0.8769	0.9897
PBC1 = OnePair/Distinct	0.8742	0.9897
PBC2 = OnePair/TwoPair	7.7633	97.9347

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	70850938	67490622
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70850938	67490622
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	70850938	67490622
Paired(QC-failed)	0	0
Read1	35425469	33745311
Read1(QC-failed)	0	0
Read2	35425469	33745311
Read2(QC-failed)	0	0
Properly Paired	70850938	67490622
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	70850938	67490622
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	125130
Np	0
N optimal	125130
N conservative	125130
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.	0.1770
Phantom Peak	50
Corr. Phantom Peak	0.1874
Argmin. Corr.	1500
Min. Corr.	0.1704
NSC	1.0386
RSC	0.3859

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	0.0601

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	0.2856
AUC	0.4952
CHANCE divergence	0.1129
Elbow Point	0.0000
JS Distance	0.5531
Synthetic AUC	0.5017
Synthetic Elbow Point	0.0904
Synthetic JS Distance	0.2654