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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'>Hi Nathan, <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'>I had already checked the probe2transcript
output – lots of alignments to introns and antisense. Nothing that points
to why this is happening though.<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'>The two tables tell me nothing more.<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'>I should point out that I ran all the same
arrays using v59 and v60 and there were no problems like this.<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'>Gavin<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'><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'> Nathan Johnson
[mailto:njohnson@ebi.ac.uk] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 10 March 2011 13:49<br>
<b><span style='font-weight:bold'>To:</span></b> Oliver, Gavin<br>
<b><span style='font-weight:bold'>Cc:</span></b> dev<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [ensembl-dev] Almost
no annotation with v61 EFG Array Mapping</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'>Gavin<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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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>To understand what these are, you need to look at them in the database.
Look at the unmapped_object table and the unmapped_reason table for more
details.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Either that, or look in the probe2transcript output, as described in
the array_mapping.txt documentation.<o:p></o:p></span></font></p>
</div>
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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'>Nath<o:p></o:p></span></font></p>
</div>
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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'><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'><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 10 Mar 2011, at 13:34, Oliver, Gavin wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
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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'>Any ideas on this Nathan? With so
many unmapped objects does it suggest some problem with the reference data i.e.
my funcgen database?<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<div>
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<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'> Oliver, Gavin <br>
<b><span style='font-weight:bold'>Sent:</span></b> 09 March 2011 08:26<br>
<b><span style='font-weight:bold'>To:</span></b> 'Nathan Johnson'<br>
<b><span style='font-weight:bold'>Cc:</span></b> dev<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [ensembl-dev] Almost
no annotation with v61 EFG Array Mapping</span></font><u1:p></u1:p><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><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'>Hi Nathan, <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Most seem to be unmapped (see the stats
below).<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Monitor looks fine.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Any ideas? Undoubtedly it will be
something simple I’m overlooking!<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>:: Logging
probesets that don't map to any transcripts - Tue Mar 8 17:25:20 2011<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>:: Updating
0 promiscuous probesets - Tue Mar 8 17:38:45 2011<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
UnmappedObjects
loaded:
598994<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
ADXBRCv2a520413 distinct ProbeSet xrefs mapped(total xrefs):
1/60856(1)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
ADXOCv1a520630 distinct ProbeSet xrefs mapped(total
xrefs): 4/120373(7)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
ADXECv1a520743 distinct ProbeSet xrefs mapped(total
xrefs): 4/111012(7)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
ADXLCv1a520538 distinct ProbeSet xrefs mapped(total
xrefs): 4/60416(10)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
ADXCRCG2a520319 distinct ProbeSet xrefs mapped(total xrefs):
2/61528(2)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
ADXPCv1a520642 distinct ProbeSet xrefs mapped(total
xrefs): 2/121563(2)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>::
HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total
xrefs): 1/54675(4)<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>:: Mapped
9/167074 transcripts - Tue Mar 8 17:38:57 2011<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><u1:p> </u1:p></span></font><o:p></o:p></p>
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<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'> Nathan Johnson
[mailto:njohnson@ebi.ac.uk] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 03 March 2011 11:09<br>
<b><span style='font-weight:bold'>To:</span></b> Oliver, Gavin<br>
<b><span style='font-weight:bold'>Cc:</span></b> dev<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [ensembl-dev] Almost
no annotation with v61 EFG Array Mapping</span></font><u1:p></u1:p><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Gavin<u1:p></u1:p><o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Have you checked the unmapped objects? These should give you a clue.<u1:p></u1:p><o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Also, you might want to check the pipeline output i.e. 'monitor'
and the ProbeAlign reports. This should show you see exactly what features you
are trying to xref.<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
<div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>Nathan Johnson<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>Scientific Programmer<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>European Bioinformatics Institute<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>Wellcome Trust Genome Campus<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>Hinxton<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><st1:place u2:st="on"><st1:city u2:st="on"><st1:City w:st="on"><st1:place
w:st="on"><font size=1 face="Times New Roman"><span style='font-size:8.0pt'>Cambridge</span></font></st1:place></st1:City></st1:city></st1:place><font
size=1><span style='font-size:8.0pt'> CB10 1SD<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>Email: <a href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a><u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'>TelNo: (+44)1223 492629<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'><u1:p> </u1:p></span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=1 face="Times New Roman"><span style='font-size:
8.0pt'><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
</div>
</div>
</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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<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>
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<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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