[BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?

[michael watson (IAH-C)]

The following (small) code works for me:

library(biomaRt)
mart <- useMart("ensembl","hsapiens_gene_ensembl")
ids <- c("ENST00000262187","ENST00000296271")
seq <- getSequence(id=ids, type="ensembl_transcript_id", mart=mart, seqType="3utr")
seq
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of mauede at alice.it [mauede at alice.it]
Sent: 28 May 2010 21:41
To: Bioconductor  List
Subject: [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx    ?

I executed the following lines several times from a script as well as pasting them in an R shell.
Systematically biomaRt is failing.
The problem is to extract the 3UTR sequences corresponding to a vector containing 1941
Ensembl Transcript numbers (some are duplicated ... is this s problem ?)
Please, find the failing instructions in the following including the ENST vector

Any suggestion is welcome. Thank you,
Maura

> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
Checking attributes ... ok
Checking filters ... ok

> genes_map[,"ensembl_transcript_id"]
   [1] "ENST00000262187" "ENST00000296271" "ENST00000346166" "ENST00000381570"

<snip>

[1937] "ENST00000400907" "ENST00000400908" "ENST00000440864" "ENST00000309042"
[1941] "ENST00000254325"

> genes_seq <- getSequence (id=genes_map[,"ensembl_transcript_id"],type="ensembl_transcript_id",
+ seqType="3utr",mart=hmart)
Error in value[[3L]](cond) :
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.



tutti i telefonini TIM!


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