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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>In some on my transcript IDS, they have a perfectly correct genomic position in UCSC<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>As an example, the NM ID - NM_001164277<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Has a valid genomic location in UCSC:<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=NM_001164277&hgt.suggest=&hgt.suggestTrack=knownGene&Submit=submit&hgsid=279134705">http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=NM_001164277&hgt.suggest=&hgt.suggestTrack=knownGene&Submit=submit&hgsid=279134705</a><b><o:p></o:p></b></p><p class=MsoNormal><b><o:p> </o:p></b></p><p class=MsoNormal><span style='color:#1F497D'>and in ENSEMBL there is no genomic position info... only the patch ID<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><a href="http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=NM_001164277">http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=1;q=NM_001164277</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:#1F497D'>So, what ideally what I would need is a way of converting the patch ID into a valid chromosome number.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>IS there an easy way of doing this?<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Best regards<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Duarte<o:p></o:p></span></p><p class=MsoNormal><b><span style='color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Duarte Molha<br><b>Sent:</b> 20 June 2012 09:20<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> [ensembl-dev] Question regarding transcript location data<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Dear developers<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>I have a script that retrieves intron and exon information from an input NM ID. It is working pretty well but I have stumbled on a few NM iDS and I would like to know what I can to correct the behaviour of the script.<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>As an example if I input this ID:<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><span style='color:black'>NM_173471<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>My script ouputs:<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>INPUT_ID CHR start end ENST_ID EXON_ID strand <o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>NM_173471 chrHG991_PATCH 66119285 66119659 ENST00000566782 ENSE00002619671 0 +1<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>NM_173471 chrHG991_PATCH 66298434 66298819 ENST00000566782 ENSE00002619173 0 +1<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>... <abbreviated><o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>However what I would have liked to have been outputted was the correct genomic location of this transcript... in this case chr3. <o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Can you tell me how I can change by script so that it gets the correct chr location instead of this PATCH ids?<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Basically I would have wanted the script to have outputted the exon/intron data from the first entry on this link:<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><a href="http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Transcript;end=2;q=NM_173471">http://www.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Transcript;end=2;q=NM_173471</a><o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Best regards,<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt;text-indent:36.0pt'>Duarte Molha<o:p></o:p></p><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div></body></html>