I have generated a new fungal assembly on a species that has been assembled before, and I am trying to translate the annotations from the old assembly to the new assembly using genemark-es within quast. The quast manual says "If a gene file is provided with -G as well, both # genes in the file covered by the assembly, and # predicted genes are reported." So it sounds like quast can link the genes in the publicly available annotation to predicted genes in my assembly, yet I cannot find any output saying which predicted gene is which with regard to the annotation. Is there anything I can do within quast to get the pre-existing annotations to show up in the predicted genes? I am wondering if there is something formatted incorrectly in my input gff3 file. The 3rd column says "gene", and the attributes are "Name", "locus_tag" and "gene".
i should add that I expect the genomes to have lots of similarity. I previously mapped my illumina reads to the old assembly with ~90% mapping rate.
I would greatly appreciate the help!