Less and less genes predicted with each iteration of SNAP/MAKER

Less and less genes predicted with each iteration of SNAP/MAKER

0

Hi

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?

Thanks


maker


annotation


snap


gene prediction


genomics

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