Last week I extracted the 3UTR sequences for a list of genes identified through their Entrez_num.
The biologist we are working with is not happy yet ... and asked me to provide the following:

Regarding the 3'UTR database I need for now the following:
 
1) UTR sequence
2) name of the gene
3) where the 3'UTR  is located in the gene sequence. In other terms the coordinates of where 3'UTR starts and ends.
Thanks

I thought it would be an easy task but I incurred in the following error:
> genes_map <- getBM(attributes=c("entrezgene","hgnc_symbol","ensembl_gene_id","ensembl_transcript_id","3_utr_start","3_utr_end"),
+ filters = "entrezgene", values=genes.ds[1:3,1], mart=hmart)
Error in getBM(attributes = c("entrezgene", "hgnc_symbol", "ensembl_gene_id",  : 
  Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed

I cannot see what I am doing wrong.
Your help is very welcome.

Thank you in advance.
Maura


tutti i telefonini TIM!


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