[ensembl-dev] Download human body map 2.0 transcript coordinates

[Jyoti Shah]

Hi Thibaut,

Thansk for your response. The schema seems complicated and I could not find
any proper documentation on this database instance. Can you point me to the
SQL queries that can help me fetch transcripts for Human body map 2.0 from
this MYSQL instance? I could see a file transcript.txt with start and end
position but there is no chromosome number attached to it. Where can I
download these build transcripts from?

Thanks,
Jyoti

On Fri, Aug 19, 2011 at 12:12 PM, Thibaut Hourlier <th3 at sanger.ac.uk> wrote:

> Hi
> you can use either the ftp site and create a local instance of the
> database:
> ftp://ftp.ensembl.org/pub/current_mysql/homo_sapiens_rnaseq_63_37/
>
> or you can use the public MySQL Server:
>
> $db = new Bio::EnsEMBL::DBAdaptor(
>        -host => 'ensembldb.ensembl.org',
>        -port => 5306O,
>        -user => 'anonymous',
>        -dbname => 'homo_sapiens_rnaseq_63_37');
> Then if you want only some tissues you can filter with the logic_name:
> +-----------------------+
> | logic_name            |
> +-----------------------+
> | adipose_rnaseq        |
> | adrenal_rnaseq        |
> | blood_rnaseq          |
> | brain_rnaseq          |
> | breast_rnaseq         |
> | colon_rnaseq          |
> | heart_rnaseq          |
> | kidney_rnaseq         |
> | liver_rnaseq          |
> | lung_rnaseq           |
> | lymph_rnaseq          |
> | ovary_rnaseq          |
> | prostate_rnaseq       |
> | skeletal_rnaseq       |
> | testes_rnaseq         |
> | thyroid_rnaseq        |
> +-----------------------+
>
> Regards
> Thibaut
>
> On Fri, 2011-08-19 at 09:18 -0400, Jyoti Shah wrote:
> > Hi,
> >
> >
> > What is the best way to download the transcripts that were built using
> > Illumina data (Human body map 2.0) explained here:
> >
> >
> >
> http://www.ensembl.info/blog/2011/05/24/human-bodymap-2-0-data-from-illumina/
> >
> >
> > I need to download the genomic coordinates.
> >
> >
> > Thanks!
> > _______________________________________________
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>
>
>
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