Entering edit mode
4.6 years ago
bgbrink ▴ 60
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.
Possible related question: Finding UTR regions in the RNA sequencing data from a non-model organism
This post eems like it is addressed to you: Ensembl insights: How are UTRs annotated?. An interesting quote:
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.