[maker-devel] Q on MAKER

[hcma]

Hi Carlson,

These are the list of directories under maker/2.31.8

bin  data  GMOD  INSTALL  lib  LICENSE  MWAS  perl  README  RELEASE  src


Where can i find augustus/? Or i have to ask my system admin to install 
this?

Thanks.

Best Regards
Karen




On 2016-02-05 14:54, Carson Holt wrote:
> 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
>>