[ensembl-dev] Difference in genomic coordinates between REFSEQ and ENSEMBL

[Duarte Molha]

Thanks Andy

I understand it is not a trivial matter... but even if the merge of the 2
datasets cannot be done (at least for now) it would be great if ENSEMBL API
could give us access to refseq data.

Maybe I am not informed well enough but I do not think there is a
straightforward way of querying for an NMid in ENSEMBL and being able to
retrieve exon and intron coordinates for that transcript. If there is
please let me know!

I believe this would be a great addition to the platform.

Best regards

Duarte

=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================


On Tue, Feb 25, 2014 at 10:34 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> Hi Duarte,
>
> So there a point that both gene sets do come from different institutes and
> funding streams and we want to maintain the best service to our users.
> Historically we have provided both gene sets separately as we felt this was
> the best way, at the time, to serve our users. However we are discussing
> how to have better links between Ensembl and RefSeq. One of the options is
> generating an über gene set similar to the one you have mentioned. This is
> still in the very early stages of discussion and is a non-trivial process.
> We will keep you & everyone else informed of any developments.
>
> All the best,
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Support Coordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 24 Feb 2014, at 21:18, Duarte Molha <duartemolha at gmail.com> wrote:
>
> > Sorry if it is a stupid question... but why not? is there some reason
> why the two datasets could not be merged?
> >
> > I would love to be able to do all my analysis using Ensembl but many of
> my clients rely on refseq entities. It would be great if they could be
> merged and be each NM transcript be identifiable directly in ensembl.
> >
> >
> > On Mon, Feb 24, 2014 at 12:34 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> > what you expect from us (WRT lowest & highest) is what we are doing. As
> for Ensembl and RefSeq transcripts the two sets of models are s
> >
> >
> >
> > =========================
> >      Duarte Miguel Paulo Molha
> >          http://about.me/duarte
> > =========================
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