[maker-devel] Q on MAKER

[hcma]

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