On 2 May 2007, at 18:43, Eric wrote:
Now that I can get biomart up and running, I'm working on using my own
data.
(gffs that load into a mysql
I'm trying to use the gff2biomart.pl script that is part of the GMOD
tools.
I'm able to load data into a database, but when I try to configure
biomart I
get errors about missing tables. Also, Marteditor complains that
there are
no data sets in the database.
Does anyone know if gff2biomart5.pl works with the most recent biomart
release?
I'm having a tough time isolating out my configuration mistakes. If
anyone
has advice I'd be grateful. I'm currently trying to load the gffs I
use to
create a seqfeature::store database (for gbrowse) into a biomart
database,
but I could just as easily dump the data out of a chado database into a
format that biomart likes.
Hi Eric,
Don Gilbert who wrote these tools (cc'ed on this email) would probably
be able
to give you best advice on their current status.
Alternatively if you dump your mart somewhere so that we can pick it up
here we'll be able
to tell you if it complies with our requirements
a.
Thanks,
--
Eric Ross
Alejandro Sánchez Lab
Howard Hughes Medical Institute
Department of Neurobiology and Anatomy
University of Utah
Wintrobe 531
[EMAIL PROTECTED]
801-585-3674
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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