[maker-devel] Q on MAKER

[Carson Holt]

Hi Karen,

There are many ways to train Augustus. I prefer to identify gene models in MAKER (GFF3) and use those to train both SNAP and Augustus. Here is a previous post on the topic —> https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ <https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ>

In the end you need to look at the SNAP and Augustus models together with evidence alignments in a genome browser (like desktop Apollo). When everything is trained well, both SNAP and Augustus models will look like each other and both seem to look like the evidence alignments.

Thanks,
Carson



> On Feb 4, 2016, at 5:52 PM, hcma <hcma at uci.edu> wrote:
> 
> 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

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