Untitled

No description

Report generated at 2020-05-04 09:05:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	164278710	199291734
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	126043603	192758941
Mapped(QC-failed)	0	0
% Mapped	76.7300	96.7200
Paired	164278710	199291734
Paired(QC-failed)	0	0
Read1	82139355	99645867
Read1(QC-failed)	0	0
Read2	82139355	99645867
Read2(QC-failed)	0	0
Properly Paired	124106755	190351557
Properly Paired(QC-failed)	0	0
% Properly Paired	75.5500	95.5100
With itself	124720528	191591556
With itself(QC-failed)	0	0
Singletons	1323075	1167385
Singletons(QC-failed)	0	0
% Singleton	0.8100	0.5900
Diff. Chroms	175132	372346
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	55536991	82947353
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	917404	947217
Paired Opt. Dupes	3497	3959
% Dupes/100	0.0165	0.0114

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55532509	82921397
Distinct Read Pairs	54615180	81974628
One Read Pair	53714071	81039698
Two Read Pairs	885269	923351
NRF = Distinct/Total	0.9835	0.9886
PBC1 = OnePair/Distinct	0.9835	0.9886
PBC2 = OnePair/TwoPair	60.6754	87.7669

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	109239174	164000272
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	109239174	164000272
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	109239174	164000272
Paired(QC-failed)	0	0
Read1	54619587	82000136
Read1(QC-failed)	0	0
Read2	54619587	82000136
Read2(QC-failed)	0	0
Properly Paired	109239174	164000272
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	109239174	164000272
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	185650
Np	0
N optimal	185650
N conservative	185650
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.	145
Corr. Est. Fragment Len.	0.1954
Phantom Peak	50
Corr. Phantom Peak	0.2188
Argmin. Corr.	1500
Min. Corr.	0.1779
NSC	1.0984
RSC	0.4272

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	0.3148

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	0.2011
AUC	0.4961
CHANCE divergence	0.1254
Elbow Point	0.0000
JS Distance	0.6977
Synthetic AUC	0.5032
Synthetic Elbow Point	0.2144
Synthetic JS Distance	0.4110