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', value
s=c("RP11-406A20.1","RP11-34P13.3","RP11-354P17.1","RP11-392A19.1","RP
11-429G19.1","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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