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Report generated at 2019-11-01 05:51:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107570864	226039766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106510753	215792208
Mapped(QC-failed)	0	0
% Mapped	99.0100	95.4700
Paired	107570864	226039766
Paired(QC-failed)	0	0
Read1	53785432	113019883
Read1(QC-failed)	0	0
Read2	53785432	113019883
Read2(QC-failed)	0	0
Properly Paired	105165170	149610145
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7600	66.1900
With itself	105901036	208550392
With itself(QC-failed)	0	0
Singletons	609717	7241816
Singletons(QC-failed)	0	0
% Singleton	0.5700	3.2000
Diff. Chroms	275837	32459107
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	44864255	41767173
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17879805	7918501
Paired Opt. Dupes	15728	11777
% Dupes/100	0.3985	0.1896

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44863361	41734528
Distinct Read Pairs	26983918	33823168
One Read Pair	15850756	27301386
Two Read Pairs	6756720	5377365
NRF = Distinct/Total	0.6015	0.8104
PBC1 = OnePair/Distinct	0.5874	0.8072
PBC2 = OnePair/TwoPair	2.3459	5.0771

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	53968900	67697344
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53968900	67697344
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53968900	67697344
Paired(QC-failed)	0	0
Read1	26984450	33848672
Read1(QC-failed)	0	0
Read2	26984450	33848672
Read2(QC-failed)	0	0
Properly Paired	53968900	67697344
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53968900	67697344
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	140999
Np	0
N optimal	140999
N conservative	140999
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.	190
Corr. Est. Fragment Len.	0.1505
Phantom Peak	50
Corr. Phantom Peak	0.1525
Argmin. Corr.	1500
Min. Corr.	0.1474
NSC	1.0209
RSC	0.6061

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	0.4019

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	0.1683
AUC	0.4932
CHANCE divergence	0.1731
Elbow Point	0.0000
JS Distance	0.7653
Synthetic AUC	0.4936
Synthetic Elbow Point	0.1817
Synthetic JS Distance	0.4428