[ensembl-dev] Genomic Sequence

[Bert Overduin]

Hello Nick,

$gene->slice gets you the slice with which the gene is associated,
i.e. the whole chromosome.

Just use $gene->seq instead.

Cheers,
Bert

On Tue, Feb 21, 2012 at 12:44 PM, Nick Fankhauser <lists at nyk.ch> wrote:
> Hi!
>
> I want to fetch the gnomic sequence of genes as reference for aligning
> sequencing reads. I'm using the following method:
>
> my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
> my $gene=$gene_adaptor->fetch_by_display_label($gene_symbol);
> my $seq = $gene->slice->seq();
>
> Now this retrieved a sequence of length 81195211 bp for TP53 as
> gene_symbol, but the genomic size of that gene should be 19143 bp.
>
> Is there anything wrong with this method and how could it be improved?
>
> Nick
> ---
> http://www.ccspmd.ethz.ch/people/fniklaus
>
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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

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