<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""></div>Yes. If you set them both, then RepeatMasker runs twice (once with each setting), and then combines the results.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 21, 2014, at 10:09 AM, Michael Campbell <<a href="mailto:michael.s.campbell1@gmail.com" class="">michael.s.campbell1@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Muriel,<div class=""><br class=""></div><div class="">By setting <span style="font-family:'Courier New',Courier,monospace;font-size:12.6666669845581px" class="">model_org=all </span>MAKER will run repeatmasker using all of RepBase. MAKER will also repeatmasker to mask with your species specific repeat library when you set <span style="font-family:'Courier New',Courier,monospace;font-size:12.6666669845581px" class="">rmlib=allRepeats.lib.</span></div><div class=""><br class=""></div><div class="">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</div><div class=""> </div><div class=""><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_control_files_explained</a>.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Mike</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Nov 21, 2014 at 9:07 AM, Muriel Gros-Balthazard <span dir="ltr" class=""><<a href="mailto:muriel.grosb@gmail.com" target="_blank" class="">muriel.grosb@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF" class="">
Hello,<br class="">
<br class="">
I generated my own library of repeats following the tutorial
provided with Maker.<br class="">
I also wanted to use all the species from the RepBase library for
the masking.<br class="">
<br class="">
It is not clear to me how this works in Maker.<br class="">
Indeed, I put both these options : <br class="">
<font face="Courier New, Courier, monospace" class="">model_org=all<br class="">
rmlib=allRepeats.lib</font><br class="">
<br class="">
However, when using RepeatMasker without Maker, you can't put both <font face="Courier New, Courier, monospace" class="">-lib allRepeats.lib</font>
and <font face="Courier New, Courier, monospace" class="">-species all</font>
as options.<br class="">
Indeed, you can only say one species when also using the -lib option
(<font face="Courier New, Courier, monospace" class="">-species arabidopsis </font>for
instance and not <font face="Courier New, Courier, monospace" class="">-species
all</font>)<br class="">
<br class="">
What about Maker ?<br class="">
<br class="">
Do I have masking of allRepeats.lib and also of all species repeats
if I put these two arguments in Maker ?<br class="">
<font face="Courier New, Courier, monospace" class="">model_org=all<br class="">
rmlib=allRepeats.lib</font><br class="">
<br class="">
Another question:<br class="">
It is said that RepeatRunner is used as well. I put the option: <font face="Courier New, Courier, monospace" class="">repeat_protein=te_proteins.fasta</font><br class="">
But realized that RepeatRunner was not installed on my computer !!!<br class="">
I had no problem to run Maker.<br class="">
So, this file of te_proteins is used rather by RepeatMasker to mask
them ?<br class="">
It is not clear to me how RepeatRunner is involved in the pipeline ?<br class="">
<br class="">
Thanks a lot for your answers,<br class="">
<br class="">
Muriel<br class="">
<br class="">
</div>
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<br class=""></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class="">Michael Campbell MS, RD.<br class="">Doctoral Candidate<br class="">Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330<br class="">ph:585-3543<br class=""><br class=""></div></div>
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