Untitled

No description

Report generated at 2020-05-21 14:48:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	177496850	177519184
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	113806519	172494915
Mapped(QC-failed)	0	0
% Mapped	64.1200	97.1700
Paired	177496850	177519184
Paired(QC-failed)	0	0
Read1	88748425	88759592
Read1(QC-failed)	0	0
Read2	88748425	88759592
Read2(QC-failed)	0	0
Properly Paired	110174399	168093297
Properly Paired(QC-failed)	0	0
% Properly Paired	62.0700	94.6900
With itself	111634876	170816950
With itself(QC-failed)	0	0
Singletons	2171643	1677965
Singletons(QC-failed)	0	0
% Singleton	1.2200	0.9500
Diff. Chroms	361163	1509587
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	42960323	73622728
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	456501	559519
Paired Opt. Dupes	1713	3080
% Dupes/100	0.0106	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42953743	73528740
Distinct Read Pairs	42497345	72972791
One Read Pair	42061218	72421080
Two Read Pairs	422877	547586
NRF = Distinct/Total	0.9894	0.9924
PBC1 = OnePair/Distinct	0.9897	0.9924
PBC2 = OnePair/TwoPair	99.4644	132.2552

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	85007644	146126418
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85007644	146126418
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	85007644	146126418
Paired(QC-failed)	0	0
Read1	42503822	73063209
Read1(QC-failed)	0	0
Read2	42503822	73063209
Read2(QC-failed)	0	0
Properly Paired	85007644	146126418
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	85007644	146126418
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	213796
Np	0
N optimal	213796
N conservative	213796
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.	0.1891
Phantom Peak	50
Corr. Phantom Peak	0.2498
Argmin. Corr.	1500
Min. Corr.	0.1710
NSC	1.1058
RSC	0.2296

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	0.1904

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	0.2254
AUC	0.4956
CHANCE divergence	0.1465
Elbow Point	0.0000
JS Distance	0.6293
Synthetic AUC	0.5014
Synthetic Elbow Point	0.0986
Synthetic JS Distance	0.3567