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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve analyzed some RNA-seq data using the extended Bin-Tian 3’UTR annotation which gives more than one isoforms.
<o:p></o:p></p>
<p class="MsoNormal">The end result does not give any coordinates though (or maybe it does but I can’t figure out what’s what).
<o:p></o:p></p>
<p class="MsoNormal">Under isoforms for the gene Hspa13 that has 3 isoforms that’s what the results show<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:black">'Hspa13:75758693.1.0','Hspa13:75758693.2.0','Hspa13:75758693.3.0'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">That means nothing to me. When I do polyA seq I can map my reads back to the genome and they are the actual polyA sites with coordinates. How can I figure out/visualize the different isoforms at UCSC? If I plug
in the bedgraph files I will probably see the big (over 40%) changes and figure out that this is the polyA site but that would take quite some effort.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Anyone has insight to this?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Thank you!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Kostas <o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">P.S. this is the entire row for the gene Tm7sf3<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="626" style="width:469.5pt;margin-left:-.75pt;border-collapse:collapse">
<tbody>
<tr style="height:15.0pt">
<td width="27" nowrap="" valign="bottom" style="width:20.15pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">event_name<o:p></o:p></span></p>
</td>
<td width="26" nowrap="" valign="bottom" style="width:19.5pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">sample1_posterior_mean <o:p></o:p></span></p>
</td>
<td width="17" nowrap="" valign="bottom" style="width:12.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample1_ci_low <o:p></o:p></span></p>
</td>
<td width="18" nowrap="" valign="bottom" style="width:13.25pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample1_ci_high <o:p></o:p></span></p>
</td>
<td width="26" nowrap="" valign="bottom" style="width:19.5pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample2_posterior_mean <o:p></o:p></span></p>
</td>
<td width="17" nowrap="" valign="bottom" style="width:12.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample2_ci_low <o:p></o:p></span></p>
</td>
<td width="18" nowrap="" valign="bottom" style="width:13.25pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample2_ci_high<o:p></o:p></span></p>
</td>
<td width="47" nowrap="" valign="bottom" style="width:34.9pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">diff <o:p></o:p></span></p>
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<td width="49" nowrap="" valign="bottom" style="width:36.6pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">bayes_factor<o:p></o:p></span></p>
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<td width="80" nowrap="" valign="bottom" style="width:59.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">isoforms <o:p></o:p></span></p>
</td>
<td width="28" nowrap="" valign="bottom" style="width:20.8pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample1_counts <o:p></o:p></span></p>
</td>
<td width="47" nowrap="" valign="bottom" style="width:35.05pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> sample1_assigned_counts <o:p></o:p></span></p>
</td>
<td width="38" nowrap="" valign="bottom" style="width:.4in;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">sample2_counts<o:p></o:p></span></p>
</td>
<td width="37" nowrap="" valign="bottom" style="width:27.85pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">sample2_assigned_counts <o:p></o:p></span></p>
</td>
<td width="12" nowrap="" valign="bottom" style="width:8.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> chrom <o:p></o:p></span></p>
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<td width="12" nowrap="" valign="bottom" style="width:8.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> strand <o:p></o:p></span></p>
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<td width="78" nowrap="" valign="bottom" style="width:58.65pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> mRNA_starts <o:p></o:p></span></p>
</td>
<td width="51" nowrap="" valign="bottom" style="width:38.45pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black"> mRNA_ends<o:p></o:p></span></p>
</td>
</tr>
<tr style="height:15.0pt">
<td width="27" nowrap="" valign="bottom" style="width:20.15pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">Tm7sf3<o:p></o:p></span></p>
</td>
<td width="26" nowrap="" valign="bottom" style="width:19.5pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.43,0.30,0.27<o:p></o:p></span></p>
</td>
<td width="17" nowrap="" valign="bottom" style="width:12.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.11,0.03,0.02<o:p></o:p></span></p>
</td>
<td width="18" nowrap="" valign="bottom" style="width:13.25pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.86,0.69,0.73<o:p></o:p></span></p>
</td>
<td width="26" nowrap="" valign="bottom" style="width:19.5pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.01,0.01,0.98<o:p></o:p></span></p>
</td>
<td width="17" nowrap="" valign="bottom" style="width:12.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.01,0.00,0.96<o:p></o:p></span></p>
</td>
<td width="18" nowrap="" valign="bottom" style="width:13.25pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.02,0.02,0.99<o:p></o:p></span></p>
</td>
<td width="47" nowrap="" valign="bottom" style="width:34.9pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0.42,0.29,-0.71<o:p></o:p></span></p>
</td>
<td width="49" nowrap="" valign="bottom" style="width:36.6pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">6.49,1.25,586.86<o:p></o:p></span></p>
</td>
<td width="80" nowrap="" valign="bottom" style="width:59.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">'Tm7sf3:146552543.1.0','Tm7sf3:146552543.2.0','Tm7sf3:146552543.3.0'<o:p></o:p></span></p>
</td>
<td width="28" nowrap="" valign="bottom" style="width:20.8pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">(0,0,0):46,(1,0,0):6,(1,1,0):2<o:p></o:p></span></p>
</td>
<td width="47" nowrap="" valign="bottom" style="width:35.05pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal" align="right" style="text-align:right"><span style="color:black">0:08<o:p></o:p></span></p>
</td>
<td width="38" nowrap="" valign="bottom" style="width:.4in;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">(0,0,0):75,(1,0,0):18,(1,1,0):3,(1,1,1):21<o:p></o:p></span></p>
</td>
<td width="37" nowrap="" valign="bottom" style="width:27.85pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">0:18,1:3,2:21<o:p></o:p></span></p>
</td>
<td width="12" nowrap="" valign="bottom" style="width:8.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">chr6<o:p></o:p></span></p>
</td>
<td width="12" nowrap="" valign="bottom" style="width:8.75pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal"><span style="color:black">-<o:p></o:p></span></p>
</td>
<td width="78" nowrap="" valign="bottom" style="width:58.65pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal" align="right" style="text-align:right"><span style="color:black">146,550,875,146,552,000,000,000,000<o:p></o:p></span></p>
</td>
<td width="51" nowrap="" valign="bottom" style="width:38.45pt;padding:0in 5.4pt 0in 5.4pt;height:15.0pt">
<p class="MsoNormal" align="right" style="text-align:right"><span style="color:black">146,552,543,146,552,000,000,000,000<o:p></o:p></span></p>
</td>
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<p class="MsoNormal"><o:p> </o:p></p>
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