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

[Thibaut Hourlier]

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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