[BioC] ChiPQC and paired-end data

[Carroll, Thomas]

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