[maker-devel] basic question on maker

[hcma]

Hi Carson,

Thanks for the link. Can maker2 be run without inputting any protein 
sequences? How to turn this off in the control files?

Also, can i run maker using Augustus and not SNAP? Again, how do i turn 
SNAP off?

Does maker also predict non-coding genes?

Thanks.

Best Regards
Karen






On 2016-01-14 12:01, Carson Holt wrote:
> Hi Karen,
> 
> All your questions may be best answered from this tutorial on the
> MAKER wiki —>
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014
> [1]
> 
> There is also a video link on the wiki page if you want to follow
> that.
> 
> Thanks,
> Carson
> 
>> On Jan 13, 2016, at 11:09 AM, hcma <hcma at uci.edu> wrote:
>> 
>> Hi,
>> 
>> I would like to include a de novo assembled transcriptome assembly
>> for running maker. The organism i am working with is fly and I am
>> wondering what is the best way to do this?
>> 
>> Do I need to get the input files for running Repeatmasker or just
>> set:
>> 
>> model_org=all
>> 
>> What's the best protein sequence file to use?
>> 
>> is ' uniprot_sprot.fasta' ok?
>> 
>> Some people use Trinity transcriptome assembly to generate a train
>> set for Augustus and then run maker again, is this a better way than
>> running maker just once?
>> 
>> Thanks for your time and any comments will be greatly appreciated.
>> 
>> Best Regards
>> Karen
>> 
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>> 
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> 
> 
> 
> Links:
> ------
> [1]
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014