I have a new bacterial strain which I assembled using SPADES and scaffolded it using SPADES. Now to annotate the scaffolds, I used RAST. RAST has given me 8000 genes. I tried to annotate the genes using RAST. Out of 8000 genes, only 1497 genes got annotated using RAST.
Could you please suggest me a way to annotate the whole 8000 genes.