[BioC] ChiPQC and paired-end data

[Ugo Borello]

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