<div dir="ltr">yes, just like the one below<div><table border="0" cellpadding="0" cellspacing="0" width="586" style="border-collapse:collapse;width:440pt">
<colgroup><col width="90" style="width:68pt">
<col width="124" span="4" style="width:93pt">
</colgroup><tbody><tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" width="90" style="height:15pt;width:68pt">1</td>
<td class="gmail-xl65" width="124" style="width:93pt">25372580</td>
<td class="gmail-xl65" width="124" style="width:93pt">rs12731221</td>
<td class="gmail-xl65" width="124" style="width:93pt">G</td>
<td class="gmail-xl65" width="124" style="width:93pt">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">1</td>
<td class="gmail-xl65">28733759</td>
<td class="gmail-xl65">rs78873359</td>
<td class="gmail-xl65">CA</td>
<td class="gmail-xl65">C</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">2</td>
<td class="gmail-xl65">1397282</td>
<td class="gmail-xl65">rs9326165</td>
<td class="gmail-xl65">G</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">2</td>
<td class="gmail-xl65">1405785</td>
<td class="gmail-xl65">rs74412499</td>
<td class="gmail-xl65">G</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">2</td>
<td class="gmail-xl65">88285154</td>
<td class="gmail-xl65">rs149707353</td>
<td class="gmail-xl65">C</td>
<td class="gmail-xl65">T</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">3</td>
<td class="gmail-xl65">85008865</td>
<td class="gmail-xl65">.</td>
<td class="gmail-xl65">C</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">3</td>
<td class="gmail-xl65">180575632</td>
<td class="gmail-xl65">rs58197854</td>
<td class="gmail-xl65">AT</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">3</td>
<td class="gmail-xl65">180575641</td>
<td class="gmail-xl65">rs114361217</td>
<td class="gmail-xl65">A</td>
<td class="gmail-xl65">T</td>
</tr></tbody></table><table border="0" cellpadding="0" cellspacing="0" width="586" style="border-collapse:collapse;width:440pt">
<colgroup><col width="90" style="width:68pt">
<col width="124" span="4" style="width:93pt">
</colgroup><tbody><tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" width="90" style="height:15pt;width:68pt">5</td>
<td class="gmail-xl65" width="124" style="width:93pt">42842763</td>
<td class="gmail-xl65" width="124" style="width:93pt">rs9686343</td>
<td class="gmail-xl65" width="124" style="width:93pt">C</td>
<td class="gmail-xl65" width="124" style="width:93pt">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">6</td>
<td class="gmail-xl65">5109555</td>
<td class="gmail-xl65">rs149371287</td>
<td class="gmail-xl65">G</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">6</td>
<td class="gmail-xl65">143929729</td>
<td class="gmail-xl65">rs6899521</td>
<td class="gmail-xl65">T</td>
<td class="gmail-xl65">C</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">7</td>
<td class="gmail-xl65">72024054</td>
<td class="gmail-xl65">rs193119573</td>
<td class="gmail-xl65">G</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">7</td>
<td class="gmail-xl65">72024079</td>
<td class="gmail-xl65">rs376943542</td>
<td class="gmail-xl65">G</td>
<td class="gmail-xl65">A</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">7</td>
<td class="gmail-xl65">89571465</td>
<td class="gmail-xl65">rs10226999</td>
<td class="gmail-xl65">C</td>
<td class="gmail-xl65">G</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" class="gmail-xl65" style="height:15pt">10</td>
<td class="gmail-xl65">11639703</td>
<td class="gmail-xl65">rs77896587</td>
<td class="gmail-xl65">G</td>
<td class="gmail-xl65">A</td>
</tr></tbody></table><br></div><div>the VEP result would like this, do not have the <span style="font-size:14px">canonical transcript. T</span>hanks a lot !</div><div><img src="cid:ii_1563559b82f386f8" alt="内嵌图片 1" width="557" height="37"><br></div><div><br></div><div><br></div><div><div style="font-size:14px">Best regard!</div><div style="font-size:14px">Lin</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-07-27 20:50 GMT+08:00 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Lin,<div><br></div><div>Can you provide an example of some input for which VEP does not provide a canonical transcript?</div><div><br></div><div>Regards</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 27 July 2016 at 08:02, 林琼芬 <span dir="ltr"><<a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Magali,<div>As you mean, a <span style="font-size:14px">canonical transcript is usually the transcript with the longest translation for a given gene, than, maybe all gene has </span>a <span style="font-size:14px">canonical transcript. However, when I use VEP-release-77, some variants has no </span><span style="font-size:14px">canonical transcript result after annotation, would you know what happen to it?</span></div><div><span style="font-size:14px;line-height:21px">Hope to hear form you.</span><span style="font-size:14px"><br></span></div><div><span style="font-size:14px"><br></span></div><div><span style="font-size:14px">Best regard!</span></div><div><span style="font-size:14px">Lin</span></div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">2016-07-26 23:06 GMT+08:00 mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Duarte,<br>
<br>
A canonical transcript is usually the transcript with the longest
translation for a given gene<br>
<a href="http://www.ensembl.org/Help/Glossary?id=346" target="_blank">http://www.ensembl.org/Help/Glossary?id=346</a><br>
<br>
In your example, XP_005244832.1 has a translation of 730 aa while
NP_003027.1 only has 728.<br>
Hence, it is chosen as the canonical transcript.<br>
<br>
As Kieron mentioned, if you want specifically curated RefSeq
annotation, it might be better to fetch all external annotations
then filter out the ones you are interested in.<br>
<br>
<br>
Regards,<br>
Magali<div><div><br>
<br>
<div>On 25/07/2016 17:07, Duarte Molha
wrote:<br>
</div>
<blockquote type="cite">
<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" style="font-size:12.8px" target="_blank">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 data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<table style="margin:0px;padding:0px;border:0px;outline:0px;font-size:14px;font-family:proxima-nova-1,proxima-nova-2,Tahoma,Helvetica,Verdana,sans-serif;vertical-align:baseline;border-spacing:0px;color:rgb(51,51,51);line-height:18.2000007629395px" border="0" cellpadding="0" cellspacing="0">
<tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;width:auto;height:30px"> </td>
</tr>
<tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:baseline;width:auto">
<div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;line-height:0"><a href="https://about.me/duarte?promo=email_sig" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;color:rgb(43,130,173);text-decoration:none;display:inline-block" target="_blank">
<table style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;border-spacing:0px" border="0" cellpadding="0" cellspacing="0">
<tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:top;width:auto;line-height:1" align="left" valign="top"><img alt="--" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block;width:0px;min-height:0px;overflow:hidden" height="0" width="0">
<div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:bold;font-style:inherit;font-size:18px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline;line-height:1;color:rgb(51,51,51)">Duarte
Molha</div>
<div style="margin:3px 0px 0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-size:12px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline"><img alt="https://" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block;width:0px;min-height:0px;overflow:hidden" height="0" width="0">about.me/duarte</div>
</td>
</tr>
<tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<td style="padding:8px 0px 0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:top;width:auto;line-height:1" align="left" valign="top">
<div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;text-align:right;min-height:4px;background-color:rgb(197,208,224)"><img src="https://d13pix9kaak6wt.cloudfront.net/signature/colorbar.png" alt="" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;float:right;display:block" height="4" width="88"></div>
</td>
</tr>
</tbody>
</table>
</a> </div>
</td>
</tr>
<tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline">
<td style="padding:0px;border:0px;outline:0px;font-style:inherit;font-size:0px;font-family:inherit;vertical-align:baseline;width:auto;height:20px"><img style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;overflow:hidden" height="1" width="1"></td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
<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><br>
<br>
<br>
<br>
<br>
<br>
> On 22 Jul 2016, at 10:47, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">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>
</div>
</div>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div></div></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div></div></div><span><font color="#888888">-- <br><div data-smartmail="gmail_signature"><div dir="ltr"><p><font face="微软雅黑, sans-serif">Arron Lin</font></p><p><font face="微软雅黑, sans-serif">BGI Research Institute</font></p><p><font face="微软雅黑, sans-serif">Email: <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a></font></p><p><font face="微软雅黑, sans-serif"></font></p><p><font face="微软雅黑, sans-serif">Beishan Industrial Zone| Yantian District| Shenzhen 518083</font></p></div></div>
</font></span></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><p><font face="微软雅黑, sans-serif">Arron Lin</font></p><p><font face="微软雅黑, sans-serif">BGI Research Institute</font></p><p><font face="微软雅黑, sans-serif">Email: <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a></font></p><p><font face="微软雅黑, sans-serif"></font></p><p><font face="微软雅黑, sans-serif">Beishan Industrial Zone| Yantian District| Shenzhen 518083</font></p></div></div>
</div>