Hi Javier.

You might find the following exchange between myself and the ENSEMBL help desk last week useful.

First my email:

Using biomaRt through R to try and retrieve the 3'UTR start and end for a set of transcript ids I get the following error.

                                                                            V1
1 Query ERROR: caught BioMart::Exception::Usage: Attribute 3utr_start NOT FOUND
Error in getBM(attributes = c("ensembl_transcript_id", "sequence_3utr_start"),  :
 Number of columns in the query result doesn't equal number of attributes in query.  This is probably an internal error, please report.

Could you tell me the easiest way to get hold of the 3'utr coordinates through the web interface please?

Thanks

Iain

And the reply:
	
	
Hello Iain,

Currently these attributes are not available from BioMart. They have
been dropped when we moved to an automated Mart building process a few
months ago. However, as many people have asked for these attributes,
they have been added again to our v52 release which, if everything goes
according to plan, should go live coming week. My apologies for any
inconvenience caused.



Hope that helps.

Iain


--- On Fri, 12/12/08, Javier Díez <jdiezperezj@gmail.com> wrote:

> From: Javier Díez <jdiezperezj@gmail.com>
> Subject: [BioC] sequence_3utr_start and sequence_3utr_end
> To: bioconductor@stat.math.ethz.ch
> Date: Friday, 12 December, 2008, 12:58 PM
> Hi everyone,
> 
> I have tried this query (just to get the 3 utr coordinates
> of transcripts of
> a given gene):
> getBM(attributes=c('sequence_3utr_end'),filters='ensembl_gene_id',value="ENSG00000...",mart=mart)
> 
> but I got this error message:
> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute
> 3utr_end NOT
> FOUND
> 
> Any idea?
> 
> Thanks
> 
> Javi
> 
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