<html><head><base href="x-msg://463/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Gavin<div><br></div><div>Setting the -utr_multiplier to 0 and omitting any other utr extension params will just use the transcript model i.e annotated UTRs. The reason why you are not getting any mappings is unclear to me at the moment as I don't really know anything about the array model you are mapping, but it maybe because the ensembl UTR annotations are conservative with repect the the transcript model which were use to design the probe/set. This is exactly why we define UTR extension parameters. More details can be found here:</div><div><br></div><div><a href="http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html">http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html</a></div><div><br></div><div>To set the 'Ensembl' defaults automatically you need to set -calculate_utrs -utr_multiplier 1</div><div><br></div><div>Nath</div><div><br></div><div><br><div><div>On 7 Dec 2010, at 12:43, Oliver, Gavin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple"><div class="Section1" style="page: Section1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Hi,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">They looked straightforward enough but I have managed to confuse myself with the UTR extensions in the EFG array mapping environment.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Basically I only want to map to a UTR if I can actually see it in the genome browser.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "> <o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">What settings should I use?<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">I tried setting all extensions to 0 but this resulted in zero annotation.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">Best,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; line-height: 24px; "><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; ">Gavin</span></font><font size="2" face="Arial"><span style="font-size: 10pt; line-height: 19px; font-family: Arial; "><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><font face="Tahoma" size="2"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><strong><b><span style="font-size: 12pt; color: blue; "><font face="Times New Roman"> </font></span></b></strong></div><strong><b><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><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.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font color="#0000ff"><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Group (UK) Limited, registered no. NI061368.<span> <span class="Apple-converted-space"> </span></span>Almac Sciences Limited, registered no. NI041550.<span> <span class="Apple-converted-space"> </span></span>Almac Discovery Limited, registered no. NI046249.<span class="Apple-converted-space"> </span><span> </span>Almac Pharma Services Limited, registered no. 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NI043067.<span> <span class="Apple-converted-space"> </span></span>All preceding companies are registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on">Northern Ireland</st1:country-region><span class="Apple-converted-space"> </span>with a registered office address of Almac House, 20 Seagoe Industrial Estate,<span class="Apple-converted-space"> </span><st1:place w:st="on"><st1:city w:st="on">Craigavon</st1:city>,<span class="Apple-converted-space"> </span><st1:postalcode w:st="on">BT63 5QD</st1:postalcode>,<span class="Apple-converted-space"> </span><st1:country-region w:st="on">UK</st1:country-region></st1:place>.<span class="Apple-converted-space"> </span><span> </span><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><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<span class="Apple-converted-space"> </span><st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region><span class="Apple-converted-space"> </span>no. 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More information on the Almac Group can be found on the Almac website:<span class="Apple-converted-space"> </span><a href="http://www.almacgroup.com" style="color: blue; text-decoration: underline; ">www.almacgroup.com</a><o:p></o:p></span></div></b></strong></font>_______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline; ">Dev@ensembl.org</a><br><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: blue; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Email: <a href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">TelNo: (+44)1223 492629</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span><br class="Apple-interchange-newline">
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