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

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, Rhoda 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.