<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">Hi,</p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">I aligned reads against UCSC genome using STAR, where UCSC gtf was used as reference annotation. However, I want to do quantitation of splicing event as per in ENSEML gtf file using MISO tool. In the homepage of MISO, it has been suggested to re-align the reads with the genome build prepared with ENSEMBL, in order to do so.</p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">My question is that if only the chromosome naming convention is different between UCSC and ENSEMBL, then just by changing the chromosome name in ENSEMBL gtf file as per in UCSC should be sufficient. Why I should need to re-align the whole reads.</p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">I will highly appreciate if someone could help me out.</p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">Thanks.</p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px"><br></p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">Best,</p><p style="margin:0px 0px 10px;color:rgb(51,51,51);font-family:'Helvetica Neue',Helvetica,Arial,sans-serif;font-size:13px;line-height:18.571430206298828px">Anil</p></div><div><div dir="ltr"><div style="font-family:georgia,serif;font-weight:bold"><span style="font-weight:normal"><b><div><span style="font-weight:normal"></span></div></b></span></div><div><b><font face="georgia, serif">Anil Kumar Kesarwani</font></b><br></div><div><i><font face="georgia, serif">Postdoctoral Associate</font></i></div><div><div><font face="georgia, serif"><br></font></div><div><font face="georgia, serif">Yale Cancer Center</font></div></div><div><font face="georgia, serif">Section of Hematology</font></div><div><font face="georgia, serif">300 George Street, # 786B<br></font></div><div><font face="georgia, serif">New Haven CT 06510</font></div><div><font face="georgia, serif"><br></font></div><div><font face="georgia, serif">Office : <span id="gc-number-83" class="" title="Call with Google Voice">+1 203 737 6990</span></font></div><div><font face="georgia, serif"><b><font><br></font></b></font></div></div></div>
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