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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'>How would I go about pulling the transcriptomic
one?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
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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'>
wmclaren@gmail.com [mailto:wmclaren@gmail.com] <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 15:27<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Oliver,
Gavin</st1:PersonName><br>
<b><span style='font-weight:bold'>Cc:</span></b> Graham Ritchie;
dev@ensembl.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - Email found in subject</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>In this case, as Graham says, the alleles will be the genomic alleles,
since you are calling from a variation_feature object.<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 2 February 2011 15:21, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName>
<<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=blue>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
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<hr size=2 width="100%" align=center>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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> <st1:PersonName w:st="on">Oliver,
Gavin</st1:PersonName>; <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><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Hi Gavin,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Thanks<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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:<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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<o:p></o:p></span></font></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
<br>
On 2 Feb 2011, at 15:02, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName>
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>
> The contents of this message and any attachments to it are confidential and
may be legally privileged. If you have received this message in error, you
should delete it from your system immediately and advise the sender.<br>
><br>
> Almac Group (UK) Limited, registered no. NI061368. Almac Sciences
Limited, registered no. NI041550. Almac Discovery Limited, registered no.
NI046249. Almac Pharma Services Limited, registered no. NI045055.
Almac Clinical Services Limited, registered no. NI041905. Almac
Clinical Technologies Limited, registered no. NI061202. Almac Diagnostics
Limited, registered no. NI043067. All preceding companies are registered
in <st1:country-region w:st="on">Northern Ireland</st1:country-region> with a
registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place
w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63
5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>.<br>
><br>
> Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>)
Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region>
no. SC154034.<br>
><br>
> Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac
Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are <st1:State
w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:State> 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><o:p></o:p></span></font></p>
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confidential and may be legally privileged. If you have received this message
in error, you should delete it from your system immediately and advise the
sender.</span></font><o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'>Almac Group (UK) Limited, registered no. NI061368.
Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited,
registered no. NI046249. Almac Pharma Services Limited, registered no.
NI045055. Almac Clinical Services Limited, registered no. NI041905.
Almac Clinical Technologies Limited, registered no. NI061202. Almac
Diagnostics Limited, registered no. NI043067. All preceding companies are
registered in <st1:country-region w:st="on">Northern Ireland</st1:country-region>
with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place
w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63
5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>.
</span></font><o:p></o:p></p>
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size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'> </span></font><o:p></o:p></p>
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size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'>Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>)
Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region>
no. SC154034. </span></font><o:p></o:p></p>
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size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span lang=EN-GB style='font-size:
12.0pt;color:black'>Almac Clinical Services LLC, Almac Clinical Technologies
LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC
are <st1:State w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:State>
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></font><o:p></o:p></p>
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<P class=MsoNormal><FONT color=#000000><SPAN lang=EN-GB style="FONT-FAMILY: 'Times New Roman'">The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><FONT color=#0000ff><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Sciences Limited, registered no. NI041550.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Discovery Limited, registered no. NI046249. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Pharma Services Limited, registered no. NI045055.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Services Limited, registered no. NI041905.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Technologies Limited, registered no. NI061202. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Diagnostics Limited, registered no. NI043067.<SPAN style="mso-spacerun: yes"> </SPAN>All preceding companies are registered in <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:country-region w:st="on">Northern Ireland</st1:country-region> with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>. <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no. SC154034. <o:p></o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><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">www.almacgroup.com</A><o:p></o:p></SPAN></P></SPAN></B></STRONG></FONT></body>
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