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

[michael watson (IAH-C)]

Hi

I parsed your entire ID list and used it in the same code I produced below, and it worked.

My id list was a vector - I wonder if your construct genes_map[,"ensembl_transcript_id"] produces not a vector, but a factor, which may cause problems for biomaRt?  I'm just guessing though.

Bioc packages are not updated automatically, no.

The best way to install bioconductor is through biocLite().

Mick

________________________________________
From: mauede at alice.it [mauede at alice.it]
Sent: 29 May 2010 15:40
To: Steffen Durinck; michael watson (IAH-C)
Cc: Bioconductor List
Subject: R: [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?

Those instructions worked fine in many other 3UTR extractions that requested a smaller number of ENSTzzzz
I would be surprised if the query vector length were a problem.
A few months ago I was suggested to download big amounts of data through one query only and then
parse the output locally.

Recently I have updated R and all the installed packages automatically.
Shall I take it that Bioconductor packages are not automatically upgraded ?
I haven't checked  that.
Anyway, on Monday I will try to upgrade biomaRt anyway. Shall I uninstall it first or may
I proceed as I did the first time following the instructions posted for Bioconductor  packages installation  ?
Thank you
Maura


-----Messaggio originale-----
Da: Steffen Durinck [mailto:sdurinck at lbl.gov]
Inviato: ven 28/05/2010 23.16
A: michael watson (IAH-C)
Cc: mauede at alice.it; Bioconductor List
Oggetto: Re: [BioC] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?

Hi Maura,

This also works for me and duplicate transcript ids shouldn't give problems,
you'll only get unique results back though.
What version of biomaRt are you running?
Would you be able to send me your complete transcript id list as an rda so I
can try the complete list?

Cheers,
Steffen

On Fri, May 28, 2010 at 1:54 PM, michael watson (IAH-C) <
michael.watson at bbsrc.ac.uk> wrote:

> 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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