[BioC] biomaRt access to ensemble genomes 11 fungi_mart_11

[Cook, Malcolm]

Sebastian,

My experience is exactly the same as yours.

I am trying to learn how to get newer ensembl marts made available via the R biomaRt interface.

Thanks for your confirmation of the issue.

~Malcolm


> -----Original Message-----
> From: thieme.sebastian at googlemail.com
> [mailto:thieme.sebastian at googlemail.com] On Behalf Of Sebastian Thieme
> Sent: Thursday, December 22, 2011 12:50 PM
> To: Cook, Malcolm
> Cc: bioconductor at r-project.org; steffen at stat.berkeley.edu;
> huber at ebi.ac.uk
> Subject: Re: [BioC] biomaRt access to ensemble genomes 11 fungi_mart_11
> 
> Hi Malcolm,
> 
> I have a older version of biomaRt 2.6.0 but I think it doesn't matter.
> If you make
> 
> library("biomaRt")
> listMarts()
> 
> you get all available marts if your mart is not listed it is not
> available right now. In my version is only fungi_mart_10 ( ENSEMBL
> FUNGI VARIATION 10 (EBI UK)) available.
> 
> fungi_mart <- useMart("fungi_mart_10")
> 
> I hope this helps a little bit.
> 
> Best
> 
> Basti
> 
> 2011/12/22 Cook, Malcolm <MEC at stowers.org>:
> > I dont see
> >
> >  fungi_mart_11  ftp://ftp.ensemblgenomes.org/pub/current/current/fungi
> /mysql/fungi_mart_11
> >
> > available when I listMarts
> >
> > Can anyone advise what I need to do to access either or both these
> ensembl genomes marts?
> >
> > Thanks!
> >
> > Malcolm Cook
> > Computational Biology - Stowers Institute for Medical Research
> >
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