[maker-devel] SNAP bootstrap training

[Timo Metz]

Hello,

I am using MAKER for a non-model organism, and I am currently trying to do
the bootstrap training for SNAP as outlined in the tutorial and the paper
for MAKER.

For the training I am using a set of ~300 sequences which are conserved (no
golden standard genes available) and have very high quality and stop
training after third round of bootstrap training.

However, it seems as training does not work properly, because when checking
the AEDs for each round of bootstrap training, they actually get worse each
round. Also the performance of snap after training is practically similar
as before training and significantly worse than using a training file for a
model organism.

Are there any suggestions what could be wrong? Is there anything special to
check or look at what is not mentioned in the tutorial?

thanks in advance

kind regards
Timo Metz
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