[maker-devel] training of gene finders using whole assembly or longest contigs?

[Quanwei Zhang]

Hello:

I am training the gene finders using the whole assembly. But it seems very
time consuming. Besides, I have to repeat the training process several
times.  Although I am running it on 25 nodes on a server, it may still take
3 (or even more) weeks for the training. I wonder how you guys train the
SNAP. Do you use the whole assembly or just select the longest contigs for
the training. If I only use longest contigs (like top 20% longest), will it
be good enough as that get by using the whole assembly? Or should I
randomly select 20% contigs for the training, for which we will have
similar length distribution as the whole assembly?

Thanks

Best
Quanwei
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