[maker-devel] Maker_opts.ctl

[Daniel Ence]

Hi Anh-Dao, 

In the maker_opts.ctl file, there are options for est and protein evidence. You’ll put all of your fasta est files together in a command separated list in the “est" option, and all of your fasta protein files in a command separated list for the “protein” option.

You’ll specify the SNAP and Genemark files in their respective options in the control file and pass the augustus and fgenesh predictions in the “pred_gff” option. 

If you have the RepeatMasker output in gff3 format you can give it to maker with the “rm_gff” option. 

If you’ve converted the cufflinks output to gff3, you can give it to maker with the “est_gff” option. I’m pretty sure Trinity only gives fasta output, so you would put that in the “est” option, along with all the other est fasta files. 

If Augustus isn’t trained for your particular organism, then you can use another organism that augustus is already trained for. The list of species that augustus has parameter files for is in the README.txt that came with Augustus. I really recommend that you run Augustus from inside maker, because then you get all the benefits of maker passing ext-based hints to augustus at runtime, which can really improve Augustus’ predictive ability. 

When you ran the augustus gene prediction separately, did you use another organism’s parameter file?

Thanks,
Daniel


On Jul 16, 2014, at 11:15 AM, Nguyen, Anh-Dao (NIH/NHGRI) [C] <nguyenan at mail.nih.gov> wrote:

> Hi,
> 
> I would like to conduct a genome annotation and have the following data:
> - Two separate RepeatMasker outputs (using -lib and -species options)
> - ESTs and RACE (fasta)
> - proteins (fasta)
> - proteins of related organisms (fasta)
> - SNAP's .hmm file (ran CEGMA, then used cegma2zff.pl to convert to ZFF format, etc. )
> - GeneMark's .hmm file (es.mod file from running gm_es.pl)
> - FGENESH++ and Augustus gene predictions. I wrote scripts to convert the outputs to .gff3 files. The reason why I ran Augustus gene prediction separately, because the genome has never been trained for Augustus.
> - Cufflinks and Trinity from RNA-Seq
> 
> Could you please let me know how can I specify parameters in the maker_opts.ctl file?
> Or do you have other suggestions to re-do the data listed above?
> 
> Thanks.
> Anh-Dao
> 
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