Tools for annotating UTRs

Question

[bgbrink]

Hello everyone,

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.

[mmfansler]

Possible related question: Finding UTR regions in the RNA sequencing data from a non-model organism

[h.mon]

This post eems like it is addressed to you: Ensembl insights: How are UTRs annotated?. An interesting quote:

If the transcript model has a CDS and a STOP codon, the 3’ UTR thus constitutes the span of sequence from that point to the end.

If you have an assembled genome, predicted genes and RNAseq data, you can map the RNAseq and intersect it with the gene models, reads mapping to the 5'- and 3'- extremities of gene models would hint at UTRs.