Hi Tim,

Not sure why you get less sequences with the getSequence query, you can add
gene_exon to your getBM query though and get the sequence for all 79 by:

gb <- getBM(attributes=c('ensembl_exon_id',
"exon_chrom_start","exon_chrom_end","gene_exon"), filters =
"ensembl_gene_id", values="ENSG00000198793", mart=ensembl, bmHeader=TRUE)


Cheers,
Steffen


On Fri, Jan 10, 2014 at 7:46 AM, Tim Smith <tim_smith_666@yahoo.com> wrote:

> Hi,
>
> I would like to retrieve the exon sequences (i.e. 5'UTR + CDS + 3'UTR) for
> a gene, alongwith the start and end positions for each exon. My short
> script is:
>
> =========
>
> library(biomaRt)
>
> ## Example gene: MTOR; ensembl id "ENSG00000198793"
> mySequence <-
> getSequence(id="ENSG00000198793",type="ensembl_gene_id",seqType="gene_exon",mart=ensembl)
>
> gb <- getBM(attributes=c('ensembl_exon_id',
> "exon_chrom_start","exon_chrom_end"), filters = "ensembl_gene_id",
> values="ENSG00000198793", mart=ensembl)
>
>
> > print(dim(seq))
> [1] 70  2
> > print(dim(gb))
> [1] 79  3
>
> ======
>
> Should I be doing something else?
>
>
> There seem to be more exons(i.e. 79) and less sequences that were
> retrieved (i.e.70). Ideally my output would have the following columns.
>
>
> ENSEMBL_ID  EXON_ID  EXON_START  EXON_END EXON_SEQUENCE
>
>
> thanks!
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>
>
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