<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="">
Hi Marc, Several groups have been doing what you described with fungal genomes for a while and it seems to be working for them. With the softmasked genome, maker will still allow EST alignments to extend into the masked regions; if it were a hard masked genome,
this wouldn’t be possible.
<div class=""><br class="">
</div>
<div class="">Let us know how it works out though!</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Daniel</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On Mar 13, 2015, at 3:48 PM, Marc Tollis <<a href="mailto:mtollis@asu.edu" class="">mtollis@asu.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">
<div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">
Hello,<br class="">
</div>
<div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">
I have a genome that has been well-annotated for species-specific repeats (using RepeatModeler, trf, and RepeatMasker), and was wondering if I could simply use the soft-masked assembly for maker annotation, in order to skip the sometimes cumbersome repeatmasking
step. Is this generally looked upon as doable, or should I just stick with using the unmasked assembly and the repeatmasking as bundled with my maker installation?<br class="">
<br class="">
</div>
<div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">
P.S. - as a spoiler, I already tried this (for snap training), but could not confirm that the masked assembly (i.e., lowercase letters) was maintained in the scaffolds as viewed in the maker output directory.<br class="">
</div>
<div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">
Thanks,<br class="">
</div>
Marc</div>
<br class="">
-- <br class="">
<div class="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Marc Tollis, Ph.D.</b></font>
<div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Post-Doctoral Research Associate</b></font></div>
<div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Arizona State University</b></font></div>
<div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">LSE 313</b></font></div>
<div class=""><font face="courier new, monospace" class=""><b style="background-color:rgb(255,255,255)" class=""><font color="#666666" class="">(480) 965-7456</font></b><br class="">
</font></div>
<div class=""><a href="mailto:marc.tollis@asu.edu" target="_blank" class=""><font face="courier new, monospace" class="">marc.tollis@asu.edu</font></a></div>
<div class=""><font face="courier new, monospace" class=""><b class=""><br class="">
</b></font></div>
<div class=""><font face="courier new, monospace" class=""><b class=""><font color="#666666" class="">website:</font> </b><a href="https://sites.google.com/site/tollisresearch/" target="_blank" class="">https://sites.google.com/site/tollisresearch/</a></font></div>
<div class=""><font face="courier new, monospace" class=""><b class=""><font color="#666666" class="">blog:
</font></b><a href="http://anolistollis.wordpress.com/" target="_blank" class="">anolistollis.wordpress.com</a></font></div>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br class="">
maker-devel mailing list<br class="">
<a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</body>
</html>