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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'>Cool, thanks.<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>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>What determines the strand it goes on?<o:p></o:p></span></font></p>
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10.0pt;font-family:Arial;color:navy'><o:p> </o:p></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'>
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 16:15<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: [SPAM] -
Re: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email found in
subject - Email found in subject - 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'>variation_feature objects have a strand just like all features in
Ensembl - most are on the forward strand (as this makes our life easier!) but
many are also on the reverse strand.<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>As I mentioned earlier, you can check this using:<o:p></o:p></span></font></p>
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<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>$vf->seq_region_strand<o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></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'>which will return a value
of 1 (forward) or -1 (reverse).<o:p></o:p></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 16:09, <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>
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<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'>Ok…</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>
<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'>So as it stands the alleles I am returning are genomic and called
via variation features. Are they always relative to the forward strand?</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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size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </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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<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 16:04<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; <a
href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re: [SPAM] - Re:
[SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email found in
subject - Email found in subject - 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'>Well yes, of
course it depends on what you mean!<o:p></o:p></span></font></p>
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<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>
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<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'>A transcript
object in Ensembl represents the region of the genome that generates the cDNA,
not the mRNA itself - this is the only thing that we'd be able to transfer the
variation_feature object to, as I don't think there is an Ensembl object
representing the mRNA.<o:p></o:p></span></font></p>
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<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>
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<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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