[maker-devel] Q on MAKER

[hcma]

Hi,

I have a genome sequence and Trinity assembly for a new species and I am 
wondering what are the best steps to take when using MAKER?

1. I used the genome sequence and all assembled Trinity sequence to do 
first run of MAKER in order to generate training set for SNAP and 
Augustus.

In maker_opts.ctl:
genome=all-chromosome-r1.04.fasta
est=Trinity.fasta
est2genome=1


2. Train SNAP

3. Train Augustus

When i train Augustus, i only supply genome and protein file, should i 
also supply the trinity file here?


4. what's the best parameter to use when running MAKER the second time 
for obtaining the final annotation? I would prefer not to use any 
external protein data.

genome=all-chromosome-r1.04.fasta
est=Trinity.fasta
est2genome=0
SNAP
Augustus

Thanks.

Best Regards
KAren