[BioC] ChiPQC and paired-end data

[Ugo Borello]

Thank you Thomas,

> 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 pretty straightforward to do using samtools view.

To be sure I understand you mean:
$ samtools view -f 64

> To retrieve consensus sets you could take the DBA object from ChIPQCexperiment
> and work from there using the Diffbind package.
> 
> dbaobject = ChIPQCexperiment at DBA
Indeed, I finally got my consensus playing with  the Diffbind package. I
needed to understand how to link properly ChIPQC with Diffbind.

Thank you again for your help.

Ugo




> From: "Carroll, Thomas" <thomas.carroll at csc.mrc.ac.uk>
> Date: Mon, 28 Jul 2014 12:16:15 +0000
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Cc: "ugo.borello at inserm.fr" <ugo.borello at inserm.fr>
> Subject: Re: [BioC] ChiPQC and paired-end data
> 
> Hi Ugo,
> 
> Sorry for the delay in reply. If you include the maintainers in the post then
> I will get a quicker notification.
> 
> 
> I usually supply blacklists as GRanges objects and this is what i have done
> when using mm9 blacklists myself form Anshul Kudaje's site. ChIPQC expects
> there to be a header when reading from a file.
>  
> 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 pretty straightforward to do using samtools view.
> 
> In the future we will include paired-end data analysis for ChIPQC. 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 = ChIPQCexperiment at DBA
> 
> 
> Then simply follow DiffBind vignette to select a suitable consensus set.
> 
> 
> 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