I am annotating a plant genome using Maker-P. I used EST and transcriptome data. I reduced the redunancy in the EST using cdhit. After three rounds of Maker( EST2genome and protein2genome followed by training SNAP twice and training Augustus twice) I now have a total set of genes. I am expecting more genes than I now have, although this is a novel genome with no reference.
How can I tell if my annotation is complete?