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Hi Duarte,<br>
<br>
RefSeq transcripts are available in Ensembl as a separate track.<br>
<br>
They are stored in the otherfeatures database and can be queried
using the Ensembl API like the ensembl gene set.<br>
<br>
All you need to do is use an otherfeatures database adaptor rather
than the core one<br>
$gene_adaptor = $registry->get_adaptor("human", "otherfeatures",
"gene");<br>
my $genes =
$gene_adaptor->fetch_all_by_logic_name('refseq_human_import');<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 25/02/2014 11:43, Duarte Molha
wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoEJnm1H-2D6+wyKxCm2Kavyej8bNntbpPZOndtUfqDVG+w@mail.gmail.com"
type="cite">
<div dir="ltr">Thanks Andy
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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!</div>
<div><br>
</div>
<div>I believe this would be a great addition to the platform.</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
Duarte</div>
</div>
<div class="gmail_extra"><br clear="all">
<div><font style="background-color:rgb(255,255,255)"
color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)"
color="#999999"> <a moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
<div class="gmail_quote">On Tue, Feb 25, 2014 at 10:34 AM, Andy
Yates <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:ayates@ebi.ac.uk" target="_blank">ayates@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Duarte,<br>
<br>
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.<br>
<br>
All the best,<br>
<br>
Andy<br>
<br>
------------<br>
Andrew Yates - Ensembl Support Coordinator<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridge CB10 1SD<br>
Tel: <a moz-do-not-send="true"
href="tel:%2B44-%280%291223-492538" value="+441223492538">+44-(0)1223-492538</a><br>
Fax: <a moz-do-not-send="true"
href="tel:%2B44-%280%291223-494468" value="+441223494468">+44-(0)1223-494468</a><br>
<a moz-do-not-send="true" href="http://www.ensembl.org/"
target="_blank">http://www.ensembl.org/</a><br>
<div class="HOEnZb">
<div class="h5"><br>
On 24 Feb 2014, at 21:18, Duarte Molha <<a
moz-do-not-send="true"
href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>>
wrote:<br>
<br>
> Sorry if it is a stupid question... but why not? is
there some reason why the two datasets could not be
merged?<br>
><br>
> 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.<br>
><br>
><br>
> On Mon, Feb 24, 2014 at 12:34 PM, Andy Yates <<a
moz-do-not-send="true" href="mailto:ayates@ebi.ac.uk">ayates@ebi.ac.uk</a>>
wrote:<br>
> 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<br>
><br>
><br>
><br>
> =========================<br>
> Duarte Miguel Paulo Molha<br>
> <a moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a><br>
> =========================<br>
</div>
</div>
<div class="HOEnZb">
<div class="h5">>
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