[maker-devel] Maker_opts.ctl

[Nguyen, Anh-Dao (NIH/NHGRI) [C]]

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