I think his problem is not access to UCSC but retrieving the exon locations.
The transformation of the coordinate systems is a simple shift() call, once
you have the exons. I don't know about Ensembl, but the GenomicFeatures
package provides the UCSC predictions.

I just realized yesterday that all of the gene predictions stored within
UCSC have the same, documented table format. Presumably rtracklayer could
convert these into something like what is provided by GenomicFeatures, but I
think GenomicFeatures already has a function for doing that (building the
DB). Could the utilities in GenomicFeatures be slightly generalized to
support the alternative gene predictions in UCSC?

Sorry for sort of hijacking the thread...

Michael

On Tue, Mar 16, 2010 at 11:20 AM, Patrick Aboyoun <paboyoun@fhcrc.org>wrote:

> 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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>>
>>
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