In this case, as Graham says, the alleles will be the genomic alleles, since you are calling from a variation_feature object.<div><br></div><div>Will<br><br><div class="gmail_quote">On 2 February 2011 15:21, Oliver, Gavin <span dir="ltr"><<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>></span> wrote:<br>
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<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">I’m using transcriptvariation->variation_feature->allele_string</span></font></p>
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<p class="MsoNormal"><b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma;font-weight:bold">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">
<a href="mailto:wmclaren@gmail.com" target="_blank">wmclaren@gmail.com</a> [mailto:<a href="mailto:wmclaren@gmail.com" target="_blank">wmclaren@gmail.com</a>] <b><span style="font-weight:bold">On Behalf Of </span></b>Will McLaren<br>
<b><span style="font-weight:bold">Sent:</span></b> 02 February 2011 15:20<br>
<b><span style="font-weight:bold">To:</span></b> Graham Ritchie<br>
<b><span style="font-weight:bold">Cc:</span></b> Oliver,
Gavin; <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
<b><span style="font-weight:bold">Subject:</span></b> [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - Email found in subject</span></font></p>
</div>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Gavin,</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">What method and object type are you using to get the alleles? It's not
clear from your email.</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Thanks</span></font></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Will</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On 2 February 2011 15:11, Graham Ritchie <<a href="mailto:grsr@ebi.ac.uk" target="_blank">grsr@ebi.ac.uk</a>> wrote:</span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Gavin,<br>
<br>
The alleles of a transcript variation always represent the genomic base change.<br>
<br>
Cheers,<br>
<br>
Graham<br>
<br>
Ensembl variation</span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
<br>
On 2 Feb 2011, at 15:02, Oliver, Gavin
wrote:<br>
<br>
> Hi,<br>
><br>
> When I pull transcript variation alleles via the API, does the allele
shown (e.g. A/T) represent the genomic base change, or the transcriptomic one?<br>
><br>
> Gavin<br>
><br>
><br>
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<p class="MsoNormal"><font color="#0000ff"><span lang="EN-GB" style="color:black;font-family:'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<span> </span>Almac Sciences Limited, registered no. NI041550.<span> </span>Almac Discovery Limited, registered no. NI046249. <span> </span>Almac Pharma Services Limited, registered no. NI045055.<span> </span>Almac Clinical Services Limited, registered no. NI041905.<span> </span>Almac Clinical Technologies Limited, registered no. NI061202. <span> </span>Almac Diagnostics Limited, registered no. NI043067.<span> </span>All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. <span> </span></span></font></p>
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<p class="MsoNormal"><span lang="EN-GB" style="color:black;font-family:'Times New Roman'">Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. </span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="color:black;font-family:'Times New Roman'">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: <a href="http://www.almacgroup.com" target="_blank">www.almacgroup.com</a></span></p>
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