<div dir="ltr">I will try and produce here the relevant parts of the script.<div><br></div><div>But I still am at loss why <span style="font-size:12.8px"> </span><a href="http://www.ncbi.nlm.nih.gov/protein/XP_005244832.1" target="_blank" style="font-size:12.8px">XP_005244832.1</a> has been tagged as canonical</div><div><br></div><div>For what you are saying is that I simply might not have cycled trough all of the refseq transcripts... but is there going to be more than one refseq transcript tagged as canonical for each gene?</div><div><br></div><div>Not sure I follow!</div><div><br></div><div>Thanks</div><div><br>Duarte</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><table border="0" cellpadding="0" cellspacing="0" 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<br><div class="gmail_quote">On 25 July 2016 at 11:58, Kieron Taylor <span dir="ltr"><<a href="mailto:ktaylor@ebi.ac.uk" target="_blank">ktaylor@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>
Can you send us a snippet of code that accesses the external database adaptor (DBEntryAdaptor?). It sounds like you may not be reading enough of your results to get the RefSeq ID you expect. We have all of the RefSeq IDs you mention associated at some level to the transcript, but some are from "RefSeq peptide predicted" for example.<br>
<br>
Kieron<br>
<br>
<br>
<br>
Kieron Taylor PhD.<br>
Ensembl Developer<br>
<br>
EMBL, European Bioinformatics Institute<br>
<div><div class="h5"><br>
<br>
<br>
<br>
<br>
<br>
> On 22 Jul 2016, at 10:47, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br>
><br>
> Hi Guys<br>
><br>
> I have a script that based on a gene symbol connects to ensembl and retrieves the canonical transcript and then does the same using the external database adaptor to get the canonical refseq transcript.<br>
><br>
> However this does not seem to give me the correct result<br>
><br>
> Take for example the gene SKI ( I am using GRCh37 assembly btw)<br>
><br>
> If you open this gene on the Ensembl browser:<br>
><br>
> <a href="http://grch37.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000157933;r=1:2159997-2161343" rel="noreferrer" target="_blank">http://grch37.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000157933;r=1:2159997-2161343</a><br>
><br>
><br>
> On SKI, Ensembl annotates as the canonical transcript: ENST00000378536<br>
><br>
> However, using by script, the external database adaptor returns the refseq XP_005244832.1 as the refseq canonical transcript, even though the correct canonical transcripts is NM_003036.3<br>
><br>
> <a href="http://www.ncbi.nlm.nih.gov/gene/6497" rel="noreferrer" target="_blank">http://www.ncbi.nlm.nih.gov/gene/6497</a><br>
><br>
> Unless I am understanding this incorrectly if the coding regions is the same length in 2 transcripts the longest should be the canonical<br>
><br>
> The longer Refseq is NM_003036.3 (has a longer 5prime UTR)<br>
><br>
> Can you help me understand this?<br>
><br>
> Many thanks<br>
><br>
> Duarte<br>
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</blockquote></div><br></div>