[BioC] biomaRt difference from biomart.org?

Rhoda Kinsella rhoda at ebi.ac.uk
Thu Dec 18 15:24:50 CET 2008

Hi Jorrit,
For your seqType, you chose "coding_gene_flank" but the gene example  
you give below is a pseudogene.
You correctly used "flank gene" on the mart interface which is why  
this worked. If you use flank gene in your BiomaRt
query then this should work.
Kind regards,

On 18 Dec 2008, at 14:08, Jorrit Boekel wrote:

> Dear list,
> I have tried to fetch 1000bp upstream sequences for a number of rat  
> genes via biomart. When using the webbased biomart this seems to  
> work alright, but when automating the process I ran into a problem:  
> for some genes, "Sequence unavailable" is returned.
> Exemplifiyng for a single gene that has this problem:
> > sqmrtjb<-useMart("ensembl","rnorvegicus_gene_ensembl")
> > getSequence(id="ENSRNOG00000005152",  
> type="ensembl_gene_id",seqType="coding_gene_flank", upstream=1000,  
> mart=sqmrtjb)
>                    V1                 V2
> 1 Sequence unavailable ENSRNOG00000005152
> On the web, I select ("Attributes->Sequences->Flank(gene), upstream  
> 1000bp, and some associated gene data (Ensembl Gene id, assoc. gene  
> name).
> Am I unknowingly querying for different things? Or is the biomaRt  
> interface connected to a different mart?
> thanks,
> jorrit
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Cambridge CB10 1SD,

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