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</o:shapelayout></xml><![endif]--></head><body lang=EN-NZ link=blue vlink=purple style='tab-interval:36.0pt'><div class=WordSection1><p class=MsoNormal>Hi,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have a RNA-<span class=SpellE>Seq</span> alignment, in the form of a BAM file, where the <span class=SpellE>reads</span> are aligned to gene models, which correspond to the stable ids of gene features in my local Ensembl instance.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Is there any way to display the BAM in Ensembl? i.e. is it possible to display this BAM which references Ensembl gene features, not the scaffolds or <span class=SpellE>contigs</span> in a Ensembl assembly/coordinate-system?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Cheers<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Ben<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><b><span style='font-size:10.0pt;mso-bidi-font-size:11.0pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'>Ben Warren</span></b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'>Research Technologist<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'><img width=210 height=70 id="_x0000_i1025" src="file:///C:\Users\hrabxw\AppData\Roaming\Microsoft\Signatures\PFR-LOGO.gif" alt="Plant & Food Research"></span><span style='mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'><o:p></o:p></span></p></div><p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'>F: +64 9 925 7001<br>ben.warren@plantandfood.co.nz<br>www.plantandfood.co.nz<br>The New Zealand Institute for Plant & Food Research Limited<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'><o:p> </o:p></span></p><div><p class=MsoNormal><b><span style='font-size:8.5pt;mso-bidi-font-size:11.0pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'>Postal Address:</span></b><span style='font-size:8.5pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'> Plant & Food Research Mt Albert<br>Private Bag 92169, Auckland, 1142, New Zealand<br></span><b><span style='font-size:8.5pt;mso-bidi-font-size:11.0pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'>Physical Address:</span></b><span style='font-size:8.5pt;font-family:"Arial","sans-serif";mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-NZ;mso-no-proof:yes'> Plant & Food Research Mt Albert<br>120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p></div></body></html>
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