[ensembl-dev] gtf2vep / cache / API

[Sabrina Legoueix Rodriguez]

Dear all,

I am working on a specie whose reference genome is not publicly 
available. I have a .gtf file for CDS annotations and a fasta file for 
the genome sequence.

I am using gtf2vep.pl to generate my .vep file from my .vcf file.

I would like to obtain the transcript nucleotide sequences of my CDSs ( 
coding sequences of my genes without UTRs...).
Is there a way to connect to the cache file generated with gtf2vep.pl 
(instead of the database registry) and use Ensembl API objects to get 
the coding sequences of my genes?

Thanks in advance for your answer.

Best regards,

-- 
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Sabrina

*Attention changement de coordonnées à partir du 15 Juin 2015:*

	

**Sabrina LEGOUEIX RODRIGUEZ**
Responsable Plateau Bioinformatique

Tél. : +33 (0) 5 61 28 57 92
sabrina.legoueix at toulouse.inra.fr <mailto:[MAIL]>
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