[BioC] warnings on easyRNASeq package

Nicolas Delhomme delhomme at embl.de
Tue Oct 2 10:19:46 CEST 2012

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.



Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at 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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