I am annotating a de novo genome using MAKER.
I first ran maker with est and protein information from a closely related species, with est2genome and protein2genome on.
I then ran MAKER with SNAP switched on, using the output of the previous step as input for snap
I then ran MAKER with SNAP switched on 3 more times.
Each time the number of predicted genes decreased. The first run predicted ~40,000 Second run ~12,000 Third run ~1200....
This cant be correct surely? I am expecting around 10,000-20,000 for my organism.
Sorry i am new to gene prediction and annotation. What i am asking is, why is SNAP drastically reducing the number of predicted genes with each iteration?
Should i just take the nearest number to what i expected and proceed into Augustus?