Untitled

No description

Report generated at 2019-12-03 16:26:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	95178238	96981564
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92908732	94057636
Mapped(QC-failed)	0	0
% Mapped	97.6200	96.9900
Paired	95178238	96981564
Paired(QC-failed)	0	0
Read1	47589119	48490782
Read1(QC-failed)	0	0
Read2	47589119	48490782
Read2(QC-failed)	0	0
Properly Paired	91690155	90998199
Properly Paired(QC-failed)	0	0
% Properly Paired	96.3400	93.8300
With itself	92270805	93287611
With itself(QC-failed)	0	0
Singletons	637927	770025
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.7900
Diff. Chroms	184089	205681
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	40796761	40192164
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1487167	554748
Paired Opt. Dupes	14933	11605
% Dupes/100	0.0365	0.0138

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40796511	40177379
Distinct Read Pairs	39309350	39622917
One Read Pair	37870167	39079490
Two Read Pairs	1392687	534171
NRF = Distinct/Total	0.9635	0.9862
PBC1 = OnePair/Distinct	0.9634	0.9863
PBC2 = OnePair/TwoPair	27.1922	73.1591

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	78619188	79274832
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78619188	79274832
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78619188	79274832
Paired(QC-failed)	0	0
Read1	39309594	39637416
Read1(QC-failed)	0	0
Read2	39309594	39637416
Read2(QC-failed)	0	0
Properly Paired	78619188	79274832
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78619188	79274832
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	150787
Np	0
N optimal	150787
N conservative	150787
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.	110
Corr. Est. Fragment Len.	0.1735
Phantom Peak	50
Corr. Phantom Peak	0.1811
Argmin. Corr.	1500
Min. Corr.	0.1693
NSC	1.0245
RSC	0.3520

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	0.1460

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	0.2936
AUC	0.4954
CHANCE divergence	0.1036
Elbow Point	0.0000
JS Distance	0.6015
Synthetic AUC	0.5056
Synthetic Elbow Point	0.1047
Synthetic JS Distance	0.2563