[BioC] ChiPQC and paired-end data

[Tom Carroll]

Ugo Borello <ugo.borello at ...> writes:

> 
> Dear Rory,
> 
> I have few basic questions about ChiPQC.
> 
> - Could I use ChiPQC with paired-end data?
> 
> - I would like to use my mouse blacklist
> https://sites.google.com/site/anshulkundaje/projects/blacklists
> MOUSE (mm9): 
> http://www.broadinstitute.org/~anshul/projects/mouse/blacklist/mm9-blacklist
> .bed.gz
> 
> I noticed that the formatting of this mm9-blacklist.bed is different from
> your blacklist_hg19.bed. For example your file has an header, not mine.
> Is it correct then to provide only a filename to my blacklist, when calling
> ChIPQC(), or is it better to import the bed file as Granges object first?
> 
> - If I understand correctly, while constructing a ChIPQCexperiment object
> and setting consensus=TRUE, a consensus peak set is generated. This
> consensus peak set consists of the peaks overlapping at least two of the
> replicate samples, correct?
> Is it possible to access this consensus peak set?
> 
> Thank you for your help and for this very useful tool,
> 
> Ugo
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at ...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 


Hi Ugo,

Sorry for the delay in reply. 

Supplying a GRanges object should work well and typically what I do. 
ChIPQC expects there to be a header when reading from a file so your
file should be good. 
 
You could use paired-end data with ChIPQC but for now this would
require you to filter your Bam file for only "first read in pair" in order
to avoid double counting and biasing the cross-coverage scores plots.
This should be straightforward to do using something like samtools view. 

In the future I do want to include paired-end data analysis for ChIPQC
 to accommodate MNAse-seq. I'm not sure how Diffbind handles paired
end data, perhaps Rory has an idea?

To retrieve consensus sets you could take the DBA object from 
ChIPQCexperiment and work from there using the Diffbind package. 

dbaobject = ChIPQCexperimentObject at DBA


best,

Tom


Thomas Carroll
Head of Bioinformatics, MRC Clinical Sciences Centre, Faculty of Medicine,
Imperial College London,Hammersmith Hospital Campus, Du Cane Road,London,W12 0NN