<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 Karen,<div class=""><br class=""></div><div class="">All your questions may be best answered from this tutorial on the MAKER wiki —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014</a></div><div class=""><br class=""></div><div class="">There is also a video link on the wiki page if you want to follow that.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 13, 2016, at 11:09 AM, hcma <<a href="mailto:hcma@uci.edu" class="">hcma@uci.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi,<br class=""><br class="">I would like to include a de novo assembled transcriptome assembly for running maker. The organism i am working with is fly and I am wondering what is the best way to do this?<br class=""><br class="">Do I need to get the input files for running Repeatmasker or just set:<br class=""><br class="">model_org=all<br class=""><br class="">What's the best protein sequence file to use?<br class=""><br class="">is ' uniprot_sprot.fasta' ok?<br class=""><br class=""><br class="">Some people use Trinity transcriptome assembly to generate a train set for Augustus and then run maker again, is this a better way than running maker just once?<br class=""><br class=""><br class="">Thanks for your time and any comments will be greatly appreciated.<br class=""><br class="">Best Regards<br class="">Karen<br class=""><br class="">_______________________________________________<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></div></blockquote></div><br class=""></div></div></body></html>