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 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

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 > > [[alternative HTML version deleted]]