[maker-devel] Repeat masking in Maker

[Carson Holt]

Yes.  If you set them both, then RepeatMasker runs twice (once with each setting), and then combines the results.

—Carson



> On Nov 21, 2014, at 10:09 AM, Michael Campbell <michael.s.campbell1 at gmail.com> wrote:
> 
> Hi Muriel,
> 
> By setting model_org=all MAKER will run repeatmasker using all of RepBase. MAKER will also repeatmasker to mask with your species specific repeat library when you set rmlib=allRepeats.lib.
> 
> For more information on what options can be used in the model_org= line of the maker_opts.ctl file you can find it here on the MAKER wiki
>  
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained>.
> 
> A few releases back Repeat runner was added internally to MAKER, so you don't have to install it seperatly. If you look in the MAKER output error you can find where MAKER called repeat runner.
> 
> Thanks,
> Mike
> 
> On Fri, Nov 21, 2014 at 9:07 AM, Muriel Gros-Balthazard <muriel.grosb at gmail.com <mailto:muriel.grosb at gmail.com>> wrote:
> Hello,
> 
> I generated my own library of repeats following the tutorial provided with Maker.
> I also wanted to use all the species from the RepBase library for the masking.
> 
> It is not clear to me how this works in Maker.
> Indeed, I put both these options : 
> model_org=all
> rmlib=allRepeats.lib
> 
> However, when using RepeatMasker without Maker, you can't put both -lib allRepeats.lib and -species all as options.
> Indeed, you can only say one species when also using the -lib option (-species arabidopsis for instance and not -species all)
> 
> What about Maker ?
> 
> Do I have masking of allRepeats.lib and also of all species repeats if I put these two arguments in Maker ?
> model_org=all
> rmlib=allRepeats.lib
> 
> Another question:
> It is said that RepeatRunner is used as well. I put the option: repeat_protein=te_proteins.fasta
> But realized that RepeatRunner was not installed on my computer !!!
> I had no problem to run Maker.
> So, this file of te_proteins is used rather by RepeatMasker to mask them ?
> It is not clear to me how RepeatRunner is involved in the pipeline ?
> 
> Thanks a lot for your answers,
> 
> Muriel
> 
> 
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> 
> 
> 
> -- 
> Michael Campbell MS, RD.
> Doctoral Candidate
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:585-3543
> 
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