problem with RepeatScout

[heiya]

Hello,

I run RepeatScout to uncover novel repeats according to the manual. However I didn't know what does the result of repeats.fa as follow mean?
>R=0
TTGTAATCGATTTTACTCTCTGGTAATCGATTACCAGAGAGTAGTAATCGATTACAA

what does R refer to?

another question is why the finally repeats.fa.filter used the command filter-stage-1.prl empty? all the reply is grateful!

[gprakhar]

Hi,

You could look at,

http://openwetware.org/wiki/Wikiomics:Repeat_finding#RepeatScout

For analysis.

or

Alternatively I would recommend use Repeat-Modeler to generate a denovo/novel repeat library and use it with Repeat Masker to analyze your genome.
Repeat Modeler uses repeat scout and some other programs internally, hence it saves you the hassle and the results are very well organized and annotated.

--
pg

[heiya]

thanks，gprakhar！

I'll try as you say!

[sunhh]

Hi,

You could look at,

http://openwetware.org/wiki/Wikiomics:Repeat_finding#RepeatScout

For analysis.

or

Alternatively I would recommend use Repeat-Modeler to generate a denovo/novel repeat library and use it with Repeat Masker to analyze your genome.
Repeat Modeler uses repeat scout and some other programs internally, hence it saves you the hassle and the results are very well organized and annotated.

--
pg

Hi gprakhar,
Could you tell me how long time RepeatModeler will take to de novo annotate a soybean genome (~973Mb)? It took me over a week now, and I can not see the end.

Thanks!