<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="">Example of training here —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors</a><div class=""><br class=""></div><div class="">You can also search the devel mailing list archives here —> <a href="https://groups.google.com/forum/#!forum/maker-devel" class="">https://groups.google.com/forum/#!forum/maker-devel</a></div><div class=""><br class=""></div><div class="">There are lots and lots of threads that go into detail on training. Note more than 2 rounds of training is not beneficial, and can actually make performance worse (there is an overtraining paradox).</div><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 Feb 10, 2017, at 9:03 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hello:<br class=""><br class=""></div>I am training the gene finders using the whole assembly. But it seems very time consuming. Besides, I have to repeat the training process several times. Although I am running it on 25 nodes on a server, it may still take 3 (or even more) weeks for the training. I wonder how you guys train the SNAP. Do you use the whole assembly or just select the longest contigs for the training. If I only use longest contigs (like top 20% longest), will it be good enough as that get by using the whole assembly? Or should I randomly select 20% contigs for the training, for which we will have similar length distribution as the whole assembly? <br class=""><br class=""></div>Thanks<br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""><div class=""><div class=""><br class=""></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></body></html>