I've generated genome indices via STAR using two Brassica napus reference genome sources: BRAD and Ensembl. Both have resulted in complications.
The BRAD gff3 varies so widely in it's attribute formatting from most gff3 files that I've hardly been able to get it to work with RNA-seq related software. Alternatively, the Ensembl genome, while formatted in a compatible way, contains only scaffolds - no chromosome information.
I know genoscope was used in the past but the website is no longer accessible.
Has anyone run into problems with the Brassica napus reference genome as well? Is the genoscope B. napus download page fully deprecated?