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<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Hi, <o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>I have rerun my array
annotations with v61. Everything seemed fine until I looked at the log
and saw that perhaps 2 probesets per array have actually mapped to a
transcript.<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Can you think of
something obvious that might have gone wrong here? The log output is below.<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Best, <o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Gavin<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>(Nathan I’m posting
here incase you didn’t receive my mail)</span></font><font size=2
face=Arial><span style='font-size:10.0pt;line-height:150%;font-family:Arial'><o:p></o:p></span></font></p>
<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'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: :: Running on probe2transcript.pl on: ni-cr-svc-slv.phar-services.com
:: :: - Mon Feb 21 09:01:02 2011<o:p></o:p></span></font></p>
<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'>:: Params are: --species homo_sapiens --transcript_dbname
homo_sapiens_core_61_37f --transcript_host ni-cr-svc-bs3 --transcript_port 3306
--transcript_user root --transcript_pass pass --xref_host ni-cr-svc-bs3
--xref_dbname homo_sapiens_funcgen_61_37f --xref_user root --xref_pass pass
--unannotated_5_utr 0 --unannotated_3_utr 0 -annotated_5_prime_extend 0
-annotated_3_prime_extend 0 --threshold 0.000005 --mismatches 2 -vendor AFFY
-format AFFY_UTR -arrays ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743
ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 -import_edb<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: No probe DB params specified, defaulting to xref params<o:p></o:p></span></font></p>
<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'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: :: Checking existing Xrefs :: ::<o:p></o:p></span></font></p>
<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'>:: You have specified -utr_multiplier and a -3|5_prime_extend,
-3|5_prime_extend will override where appropriate<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Setting 3 unannotated UTR length to 0<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Setting 5 unannotated UTR length to 0<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Identified 167074 transcripts for probe mapping<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Allowed mismatches = 2<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Caching arrays per ProbeSet - Mon Feb 21 09:01:21 2011<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Performing overlap analysis. % Complete:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: 0 :: 1 :: 2 :: 3 :: 4 :: 5 :: 6 :: 7 ::
8 :: 9 :: 10 :: 11 :: 12 :: 13 :: 14 :: 15 :: 16 :: 17 ::
18 :: 19 :: 20 :: 21 :: 22 :: 23 :: 24 :: 25 :: 26 :: 27 ::
28 :: 29 :: 30 :: 31 :: 32 :: 33 :: 34 :: 35 :: 36 :: 37 ::
38 :: 39 :: 40 :: 41 :: 42 :: 43 :: 44 :: 45 :: 46 :: 47 ::
48 :: 49 :: 50 :: 51 :: 52 :: 53 :: 54 :: 55 :: 56 :: 57 ::
58 :: 59 :: 60 :: 61 :: 62 :: 63 :: 64 :: 65 :: 66 :: 67 ::
68 :: 69 :: 70 :: 71 :: 72 :: 73 :: 74 :: 75 :: 76 :: 77 ::
78 :: 79 :: 80 :: 81 :: 82 :: 83 :: 84 :: 85 :: 86 :: 87 ::
88 :: 89 :: 90 :: 91 :: 92 :: 93 :: 94 :: 95 :: 96 :: 97 ::
98 :: 99 ::<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Failed to extend 1 transcripts<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Seen 0 5 prime UTRs with and average length of 0<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Seen 0 3 prime UTRs with and average length of 0<o:p></o:p></span></font></p>
<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'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: :: Writing ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743
ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 Xrefs
:: :: - Mon Feb 21 18:26:37 2011<o:p></o:p></span></font></p>
<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'>:: Logging probesets that don't map to any transcripts - Mon Feb
21 18:26:37 2011<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Updating 0 promiscuous probesets - Mon Feb 21 18:40:28 2011<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: UnmappedObjects loaded: 598994<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: ADXBRCv2a520413 distinct ProbeSet xrefs mapped(total xrefs):
1/60856(1)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: ADXOCv1a520630 distinct ProbeSet xrefs mapped(total xrefs):
4/120373(7)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: ADXECv1a520743 distinct ProbeSet xrefs mapped(total xrefs):
4/111012(7)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: ADXLCv1a520538 distinct ProbeSet xrefs mapped(total xrefs):
4/60416(10)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: ADXCRCG2a520319 distinct ProbeSet xrefs mapped(total xrefs):
2/61528(2)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total xrefs):
1/54675(4)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: ADXPCv1a520642 distinct ProbeSet xrefs mapped(total xrefs):
2/121563(2)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>:: Mapped 9/167074 transcripts - Mon Feb 21 18:40:39 2011<o:p></o:p></span></font></p>
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