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Hello,<br>
<br>
I generated my own library of repeats following the tutorial
provided with Maker.<br>
I also wanted to use all the species from the RepBase library for
the masking.<br>
<br>
It is not clear to me how this works in Maker.<br>
Indeed, I put both these options : <br>
<font face="Courier New, Courier, monospace">model_org=all<br>
rmlib=allRepeats.lib</font><br>
<br>
However, when using RepeatMasker without Maker, you can't put both <font
face="Courier New, Courier, monospace">-lib allRepeats.lib</font>
and <font face="Courier New, Courier, monospace">-species all</font>
as options.<br>
Indeed, you can only say one species when also using the -lib option
(<font face="Courier New, Courier, monospace">-species arabidopsis </font>for
instance and not <font face="Courier New, Courier, monospace">-species
all</font>)<br>
<br>
What about Maker ?<br>
<br>
Do I have masking of allRepeats.lib and also of all species repeats
if I put these two arguments in Maker ?<br>
<font face="Courier New, Courier, monospace">model_org=all<br>
rmlib=allRepeats.lib</font><br>
<br>
Another question:<br>
It is said that RepeatRunner is used as well. I put the option: <font
face="Courier New, Courier, monospace">repeat_protein=te_proteins.fasta</font><br>
But realized that RepeatRunner was not installed on my computer !!!<br>
I had no problem to run Maker.<br>
So, this file of te_proteins is used rather by RepeatMasker to mask
them ?<br>
It is not clear to me how RepeatRunner is involved in the pipeline ?<br>
<br>
Thanks a lot for your answers,<br>
<br>
Muriel<br>
<br>
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