[maker-devel] Q on MAKER

[Carson Holt]

Augustus gives you an entire directory rather than just a single file like SNAP.  You have to take the directory and copy it to the .../augustus/config/species/ directory.

Example:
…/augustus/config/species/arabidopsis/

Then ‘arabidopsis’ would be the species name to use with MAKER.

Sometimes you may have to do a second round of both SNAP and Augustus training (called bootstrapping). Look at the models you get after the first round, and if they look good then, the second round is probably not going top be beneficial.

—Carson



> On Feb 5, 2016, at 3:42 PM, hcma <hcma at uci.edu> wrote:
> 
> Hi Dr Holt,
> 
> Thanks for the email. Here is my pipeline, does it seems acceptable? Any comments is welcome and much appreciated.
> 
> 
> 1. Use maker to generate training gene set:
> 
> genome=all-chromosome-r1.04.fasta
> est=Trinity.fasta
> est2genome=1
> 
> 
> 2. Use output of Maker to train SNAP:
> 
> maker2zff dwil-all-chromosome-r1.04.all.gff
> fathom genome.ann genome.dna –gene-stats
> fathom genome.ann genome.dna –categorize 1000
> fathom genome.ann genome.dna –gene-stats
> fathom uni.ann uni.dna –export 1000 –plus
> hmm-assembler.pl genome . > dwil_genome.hmm
> 
> 
> 3. Use output of Maker to train Augustus on their webserver:
> 
> File used:
> 
> Upload ‘export.dna’ as the genome file
> Upload ‘export.aa’ as the protein file
> 
> 
> 
> 4. second and final Maker run:
> 
> 
> genome=all-chromosome-r1.04.fasta
> est=Trinity.fasta
> est2genome=0
> Snaphmm=output of 2
> 
> How do i incorporate the output of training set of gene from Augustus web server here into this step 4?
> 
> Thanks for your time.
> 
> Best Regards
> Karen
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 2016-02-05 06:36, Carson Holt wrote:
>> 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
>> [1]
>> 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
>> Links:
>> ------
>> [1]
>> https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ
>