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<span id="mailbox-conversation"><div>Hi Folks,</div>
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<div>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>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>Any help would (as always) be greatly appreciated!</div>
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<div>Best,</div>
<div>Jason Gallant</div></span><div class="mailbox_signature">
<br>—<br>Dr. Jason R. Gallant<div>Assistant Professor</div>
<div>Room 38 Natural Sciences<br><div>Department of Zoology</div>
<div>Michigan State University</div>
<div>East Lansing, MI 48824</div>
<div>jgallant@msu.edu</div>
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<div>office: 517-884-7756</div>
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