Howdy,<br>    I am working with a genome that is not well annotated and when I tried to obtain the 3&#39;UTR of around 500 genes from Biomart, I only obtain a few (around 20). What would be the easiest way to obtain the 3&#39;UTR using my RNA-seq data (I have 15 samples sequenced)?. I can see the reads on the genomic browser, but I need an automated process. I tried to get the untranscribed gene from Biomart, then the CDS and cDNA and align them, to see the 3&#39;UTR, but still not able get anything after the stop code. Does anyone have experience with it? I also saw that there a lot of genes with &quot;wrong&quot; annotation within the coding region.<br clear="all">
Thank you.<br><br><br><br>-- <br><b>Luciano Cosme</b><br><br>---------------------------------------------<br>PhD Candidate<br>Texas A&amp;M Entomology<br>Vector Biology Research Group<br><a href="http://www.lcosme.com" target="_blank">www.lcosme.com</a><br>
979 845 1885<br><a href="mailto:cosme@tamu.edu" target="_blank">cosme@tamu.edu</a><br>---------------------------------------------<br><br>