[BioC] exon genomic coordinates

[Hans-Rudolf Hotz]

Hi John

You can use the BioMart database, which you can access with the biomaRt 
package to get all exons for all transcripts for a given giene, eg:

library(biomaRt)
ensembl = useMart("ensembl")
#assuming you are interested in mouse
mouse.ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl)

getBM(attributes = 
c("chromosome_name","exon_chrom_start","exon_chrom_end","ensembl_exon_id","ensembl_transcript_id","ensembl_gene_id"), 
filters = 'mgi_symbol', values=c("KIT"),mart=mouse.ensembl)


Hope this helps

Hans-Rudolf

On 11/21/2013 09:14 AM, array chip wrote:
> Hi,
>
>
> Can anyone suggest how to retrieve the genomic coordinates for all exons for a given gene by say gene symbol? For example, how to retrieve the coordinates for all 21 exons for gene KIT?
>
> Thanks
>
> John
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