Hi Nico,

Thanks for your prompt reply.
I'm currently trying easyRNASeq out with human (Hsapiens) as my reference.
It should be available as part of a BSgenome package.

Let me know if you need anything else.
Much thanks!

Mun Hua


On Tue, Oct 2, 2012 at 4:19 PM, Nicolas Delhomme <delhomme@embl.de> wrote:

> Dear Mun Hua,
>
> I've Cc'ed the Bioconductor mailing list as it might be of interest to
> others.
>
> It is still on my TODO list to add this information into the vignette. I
> have come up with an example use case and need to insert it into the
> vignette. Moreover, we have started some code consolidation with other
> packages that will probably affect how this is done in the future. There
> are at the moment no commands or parameters in easyRNASeq that will cure
> your annotation for you. You need to come up with your own method, which
> IMO is the best approach as (a) I won't be able to think of all the
> possible use cases (b) you're certainly much more familiar with the
> organism you are using than I am so you would know best the possible
> caveats (e.g. trans-splicing in fruitfly). There are methods existing in
> other packages: GenomicRanges for example (you can look at the PDF on this
> page: http://bioconductor.org/packages/2.10/bioc/html/GenomicRanges.html,
> see the summarizeOverlaps related PDFs in the Documentation part of the
> page).
>
> What I can propose you is that we process your annotation file together
> (off-list) as it will help me finalize that vignette use case. If you
> agree, just tell me what organism you are working with and we can get
> started. If it's an organism not available as a Bioc BSgenome package,
> please point me to where I can get the chromosome and gene information.
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme@embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
>
>
>
>
>
> On 1 Oct 2012, at 17:46, Mun Hua Tan wrote:
>
> > Hi,
> >
> > I'm using easyRNASeq to generate count tables and I noticed warnings
> suggesting overlaps in the annotation. I'm aware that you mentioned you've
> added instructions in the vignette on how to deal with these overlaps, but
> I can't seem to find it anywhere in the vignette. The commands with and
> without adapting the annotation look the same to me.
> >
> > Can you please point out what command or parameter can be set to solve
> this warnings issue?
> >
> > Much thanks,
> > Mun Hua
>
>

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