[maker-devel] basic question on maker

[Carson Holt]

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 <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014>

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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