[maker-devel] Repeat masking in Maker

[Michael Campbell]

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
.

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> 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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