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

[Andy Yates]

Hi Duarte,

In addition to what Mag says you can also do the following:

my $ta = Bio::EnsEMBL::Registry->get_adaptor('human', 'otherfeatures', 'transcript');
my $transcript = $ta->fetch_by_stable_id('NM_001101426.3');

You can also get this via the rest API like so:

http://beta.rest.ensembl.org/lookup/id/NM_001101426.3?object_type=Transcript;db_type=otherfeatures;species=human;format=full;expand=1

RefSeqs are not indexed by our internal lookup for REST which is why you have to manually tell it the object type, database it lives in & species.

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 25 Feb 2014, at 11:55, mag <mr6 at ebi.ac.uk> wrote:

> Hi Duarte,
> 
> RefSeq transcripts are available in Ensembl as a separate track.
> 
> They are stored in the otherfeatures database and can be queried using the Ensembl API like the ensembl gene set.
> 
> All you need to do is use an otherfeatures database adaptor rather than the core one
> $gene_adaptor = $registry->get_adaptor("human", "otherfeatures", "gene");
> my $genes = $gene_adaptor->fetch_all_by_logic_name('refseq_human_import');
> 
> 
> Hope that helps,
> Magali
> 
> On 25/02/2014 11:43, Duarte Molha wrote:
>> 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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