I have high quality sequencing data, as well as RNA-seq data. We successfully assembled a de novo genome, however the automatic gene prediction (e.g. with AUGUSTUS) does not give any information about the UTRs. I think using the RNA-seq data it should be possible to annotate many of UTRs correctly,. However, I could not find any tools for this, which I find hard to believe.
Does anyone know a tool for (semi-)automatic annotation of UTRs? We are particularly interested in the 5'UTR.