Untitled

No description

Report generated at 2020-06-05 20:30:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	76771150	91343384
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64894596	89445671
Mapped(QC-failed)	0	0
% Mapped	84.5300	97.9200
Paired	76771150	91343384
Paired(QC-failed)	0	0
Read1	38385575	45671692
Read1(QC-failed)	0	0
Read2	38385575	45671692
Read2(QC-failed)	0	0
Properly Paired	62706550	87213841
Properly Paired(QC-failed)	0	0
% Properly Paired	81.6800	95.4800
With itself	64017242	88898599
With itself(QC-failed)	0	0
Singletons	877354	547072
Singletons(QC-failed)	0	0
% Singleton	1.1400	0.6000
Diff. Chroms	113980	153716
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	24986856	38419123
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4870507	536213
Paired Opt. Dupes	8025	12817
% Dupes/100	0.1949	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24986067	38404764
Distinct Read Pairs	20115717	37868795
One Read Pair	16276209	37344268
Two Read Pairs	3030074	515141
NRF = Distinct/Total	0.8051	0.9860
PBC1 = OnePair/Distinct	0.8091	0.9861
PBC2 = OnePair/TwoPair	5.3716	72.4933

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	40232698	75765820
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40232698	75765820
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	40232698	75765820
Paired(QC-failed)	0	0
Read1	20116349	37882910
Read1(QC-failed)	0	0
Read2	20116349	37882910
Read2(QC-failed)	0	0
Properly Paired	40232698	75765820
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	40232698	75765820
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	94879
Np	0
N optimal	94879
N conservative	94879
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.	0.2044
Phantom Peak	50
Corr. Phantom Peak	0.2354
Argmin. Corr.	1500
Min. Corr.	0.1754
NSC	1.1654
RSC	0.4838

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	0.2450

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	0.2105
AUC	0.4936
CHANCE divergence	0.1645
Elbow Point	0.0000
JS Distance	0.6864
Synthetic AUC	0.4954
Synthetic Elbow Point	0.2581
Synthetic JS Distance	0.3835