<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Carson et al.,<div><br></div><div>Thanks again for a great suite tools!</div><div><br></div><div>We're using MAKER now to generate gene models (and model fragments) for a ciliate, the models for which we'll be using to generate a high-quality protein database for searches with mass spec.</div><div><br></div><div>I bootstrapped the process using the core set of proteins with CEGMA, then trained SNAP. After the final round of running MAKER, I get about 1100 evidence-based models and 34K ab-initio. And that's fine (for now).</div><div><br></div><div>I am able to collect the fasta files for both transcripts and proteins (evidence-based and ab-initio) without problem.</div><div><br></div><div>My problem is that when I use the gff3_merge script, I only get annotations for the evidence-based models. I'm not sure why the ab-initio model annotations are being collected. I've tried using and not the '-g' switch, but this doesn't seem to make a difference.</div><div><br></div><div>Thoughts?</div><div><br></div><div>Tx,</div><div>B</div><div><br></div><div><div><div>
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margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Bob Freeman, Ph.D.</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Acorn Worm Informatics, Kirschner lab</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Systems Biology, Alpert 524</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Harvard Medical School</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">200 Longwood Avenue</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Boston, MA 02115</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">617/432.2294, vox</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><span class="Apple-style-span" style="font-size: medium; "><div><div><div><div><div><div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br><div style="font-style: normal; ">"Sorry I'm late. Oh, God, that sounded insincere. I'm late."</div><div><span class="Apple-tab-span" style="font-style: normal; white-space: pre; "> </span>-- Karen Walker, from<span class="Apple-converted-space"> </span><i>Will and Grace</i></div><div style="font-style: normal; "><br></div></span></font></div></div></div></div></div></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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