The GenomicFeatures package in BioC 2.6 (w/ R-devel) supports the
following set of transcript tables provided by UCSC:
track subtrack
knownGene UCSC Genes <NA>
knownGeneOld3 Old UCSC Genes <NA>
wgEncodeGencodeManualRel2 Gencode Genes Genecode Manual
wgEncodeGencodeAutoRel2 Gencode Genes Genecode Auto
wgEncodeGencodePolyaRel2 Gencode Genes Genecode PolyA
ccdsGene Consensus CDS <NA>
refGene RefSeq Genes <NA>
xenoRefGene Other RefSeq <NA>
vegaGene Vega Genes Vega Protein Genes
vegaPseudoGene Vega Genes Vega Pseudogenes
ensGene Ensembl Genes <NA>
acembly AceView Genes <NA>
sibGene SIB Genes <NA>
nscanPasaGene N-SCAN N-SCAN PASA-EST
nscanGene N-SCAN N-SCAN
sgpGene SGP Genes <NA>
geneid Geneid Genes <NA>
genscan Genscan Genes <NA>
exoniphy Exoniphy <NA>
augustusHints Augustus Augustus Hints
augustusXRA Augustus Augustus De Novo
augustusAbinitio Augustus Augustus Ab Initio
acescan ACEScan <NA>
Patrick
On 3/16/10 1:18 PM, Michael Lawrence wrote:
> 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 <[email protected]
> <mailto:[email protected]>> 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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