<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=""><div class="">I ran a few est2genome runs with a cufflinks file i just generated and did not get any issues for EST based gene models.</div><div class=""><br class=""></div><div class="">I’d like to at least have your test set to see if I can duplicate what you are seeing.</div><div class=""><br class=""></div><div class="">Use this to upload the job files then I can just run it from my server here —> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi" class="">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 3, 2015, at 11:13 AM, Jason Gallant <<a href="mailto:jgallant@msu.edu" class="">jgallant@msu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<span id="mailbox-conversation" class=""><div class="">Hi Folks,</div>
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<div class="">I’ve nearly succeeded at getting MAKER to run on AWS— I’ve been checking the output files, and have noticed that none of my RNAseq data was incorporated on the run. I used Cufflinks to perform alignments of libraries from several tissues, ran the accessory script cufflinks2gff3 for each tissue, then concatenated the resulting gff3 files. I even ran the accessory script gff3merge to check that the resulting file was properly formatted.</div>
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<div class="">For options, I set est2genome=1 and est_gff=cufflinks.gff. I only get protein2genome and repeatmasker evidence in my resulting maker gff3 file, and the genes predicted by these. Is there another option that I need to enable in order to use my est_gff file? I’m trying to get a set of genes to train the predictors for my next step.</div>
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<div class="">Any help would (as always) be greatly appreciated!</div>
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<div class="">Best,</div>
<div class="">Jason Gallant</div></span><div class="mailbox_signature">
<br class="">—<br class="">Dr. Jason R. Gallant<div class="">Assistant Professor</div>
<div class="">Room 38 Natural Sciences<br class=""><div class="">Department of Zoology</div>
<div class="">Michigan State University</div>
<div class="">East Lansing, MI 48824</div>
<div class=""><a href="mailto:jgallant@msu.edu" class="">jgallant@msu.edu</a></div>
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<div class="">office: 517-884-7756</div>
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