[maker-devel] repeat masking and repeat libraries

[Xabier Vázquez Campos]

Hi there,

First, a general question. Probably kind of silly but I prefer to be
sure... When you browse RepBase, for example in fungi, all the repeats are
marked as Eukaryota (Ancestral) or under the name of the species but no
other taxa ranks are indicated. Does RepeatMasker recognise orders,
families etc? or in my case should I stick with model_org=fungi?

I've been trying to create a repeat libraries specific for my genomes and I
did't have any luck with the programs described in the Basic
<http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Basic>
and advanced
<http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Advanced>
tutorials (neither in my computer or in the cluster), reporting errors at
all times, with exception of RepeatModeler, which ran with no problems. Is
the output from RepeatModeler enough to improve the masking? It is not the
best option I guess, but better than just the RepBase libraries by
themselves, isn't it?

Thank you for your time,

Xabier

-- 
Xabier Vázquez Campos
*PhD Candidate*
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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