[maker-devel] repeat masking and repeat libraries

[Michael Campbell]

Hi Xabier,

I haven't seen orders or families documented for repeatmasker with repbase.
Fungi seems safe to me.

If you want to give yourself a little more peace of mind about the
repeatmodeler library you can blast it to database of known fungal proteins
and remove the entries int he library that have strong hits to a known
protein to avoid over-masking.

Mike

On Fri, Jan 16, 2015 at 10:04 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Using both RepBase and a RepeatModeler produced library should be
> sufficient, especially for fungi.
>
> —Carson
>
>
> On Jan 16, 2015, at 3:11 AM, Xabier Vázquez Campos <xvazquezc at gmail.com>
> wrote:
>
> 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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-- 
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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