Dear Ian,

You are right, these "Ids" are clone based VEGA gene name (please see http://www.ensembl.org/info/genome/genebuild/genome_annotation.html for detail). You can filter on these gene name in the ensembl mart:

mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

vega_trans_chr_locs <- getBM(attributes=c('ensembl_gene_id', 'clone_based_vega_gene_name', 'chromosome_name', 'start_position', 'end_position', 'strand'), filters='clone_based_vega_gene_name', values=c("RP11-406A20.1","RP11-34P13.3","RP11-354P17.1","RP11-392A19.1","RP11-429G19.1","RP11-432I13.2","RP11-74C1.1","RP3-410C9.2","RP3-477H23.1","RP5-1043L13.1"), mart=mart)

> vega_trans_chr_locs
  ensembl_gene_id clone_based_vega_gene_name chromosome_name start_position end_position strand
1 ENSG00000237626              RP11-406A20.1               9       92740564     92749768      1
2 ENSG00000238129                RP3-410C9.2              20       26171625     26174582      1
3 ENSG00000228340              RP5-1043L13.1              20       58662895     59102516      1

Hope this helps,
Regards,
Thomas
On 12 May 2014, at 14:09, Iain Gallagher <iaingallagher@btopenworld.com> wrote:

> Hi List
> 
> I have a bunch of ids of the form above. What are these ids and what would be the filter option for mappin these to chromosomal coordinates using biomaRt (if it can be done)?
> 
> Looking on Ensembl, VEGA and Google would suggest that these are clone based VEGA gene ids so I tried querying VEGA using 'vega_gene_id' or 'vega_transcript_id' as a filter with no success.
> 
> Full list of worrisome ids:
> 
> RP11-406A20.1, RP11-34P13.3,  RP11-354P17.1, RP11-392A19.1, RP11-429G19.1, RP11-432I13.2, RP11-74C1.1,  
> RP3-410C9.2,   RP3-477H23.1,  RP5-1043L13.1
> 
> Current code:
> vega_mart <- useMart('vega', dataset='hsapiens_gene_vega')
> 
> vega_trans_chr_locs <- getBM(attributes=c('vega_gene_id', 'chromosome_name', 'start_position', 'end_position', 'strand'), filters=c('vega_gene_id'), values=data_in$symbol, mart=vega_mart)
> 
> 
> Thanks for any help.
> 
> Best
> 
> iain
> 
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> 
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom


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