[ensembl-dev] Converting genomic coordinates to transcript coordinates

[Will McLaren]

Hi Gavin,

You will need a transcript mapper object:

my $tm = $transcript->get_TranscriptMapper;

my @coords = $tm->genomic2cdna($start, $end, $strand);

This returns a list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap
objects.

Cheers

Will

On 26 January 2011 12:46, Oliver, Gavin <gavin.oliver at almacgroup.com> wrote:

>  Hi,
>
>
>
> I’m guessing the answer will be transfer or transform but can someone
> advise on the fastest way to convert feature start/end coordinates from
> genomic to transcript-based?  I don’t want to mistakenly do it in an
> unnecessarily time/resource-consuming manner.
>
>
>
> Best,
>
>
>
> Gavin
>
>
>
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