<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Ab initio models without evidence support are not considered final models by default (newly trained ab initio predictors tend to have a very high false positive rate).</div><div><br></div><div>If you really want the ab initio models without support to upgraded, set the keep_preds=1 in the maker_opts.ctl file. All ab inito models are also stored in the GFF3 as match/mtach_part features for reference purposes not gene/mRNA/exon/CDS.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Freeman, Robert M." <<a href="mailto:Bob_Freeman@hms.harvard.edu">Bob_Freeman@hms.harvard.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 19 March, 2013 9:03 AM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Failing to recoup all gff annotations, including ab-initio<br></div><div><br></div><div><div 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><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; 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"><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; ">-----------------------------------------------------</div><div style="font-style: normal; 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"></div><br></div></div></div></div>_______________________________________________
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