[Bioc-sig-seq] mapping coordinates

[Patrick Aboyoun]

Jason,
The rtracklayer provides an interface to the UCSC browser. In particular 
rtracklayer::export can export a SimpleRleList to a bed file that you 
can upload to UCSC.

Patrick


On 3/16/10 6:50 AM, Jason Lu wrote:
> Hi,
>
> I would like get suggestions on what is the best way to do this. I
> have a "SimpleRleList" object, in which the range coordinates are
> relevant to an ensembl transcript (ranges from 1 to the total length
> of the transcript). I would like to show my data on the UCSC browser,
> so I need to map those coordinates to the genome. Currenty I wrote my
> own script to do this, based on the exon locations from biomart. There
> got to be an easy way to do this, but don't seem to find a quick
> answer. Sorry if this has been answered.
>
> Thanks.
>
> Jason
>
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