I am working with a genome that is not well annotated and when I tried
to obtain the 3'UTR of around 500 genes from Biomart, I only obtain a few
(around 20). What would be the easiest way to obtain the 3'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'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
"wrong" annotation within the coding region.
Thank you.

*Luciano Cosme*

PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
979 845 1885
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