<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="">Using both RepBase and a RepeatModeler produced library should be sufficient, especially for fungi.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 16, 2015, at 3:11 AM, Xabier Vázquez Campos <<a href="mailto:xvazquezc@gmail.com" class="">xvazquezc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi there,<br class=""><br class=""></div>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? <div class=""><br class="">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 <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Basic" target="_blank" class="">Basic</a> and <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Advanced" target="_blank" class="">advanced</a> 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?<br class=""><br class=""></div><div class="">Thank you for your time,<br class=""><br class=""></div><div class="">Xabier<br clear="all" class=""></div><div class=""><div class=""><div class=""><br class="">-- <br class=""><div class="">Xabier Vázquez Campos<br class=""><i class="">PhD Candidate</i><br class="">Water Research Centre<br class="">School of Civil and Environmental Engineering<br class="">
The University of New South Wales<br class="">Sydney NSW 2052 AUSTRALIA<br class=""></div>
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