biomaRt mapping id RP5-1043L13.1
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@iain-gallagher-2532
Last seen 8.7 years ago
United Kingdom
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 [[alternative HTML version deleted]]
biomaRt Vega biomaRt Vega • 1.1k views
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Thomas Maurel ▴ 800
@thomas-maurel-5295
Last seen 13 months ago
United Kingdom
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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 [[alternative HTML version deleted]]
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