[galaxy-user] Obtain 3' UTR

Howdy, 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.