<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div><br><div><div>On 01 Nov 2016, at 2:34 AM, Allison Fuiten <<a href="mailto:allisonfuiten@gmail.com">allisonfuiten@gmail.com</a>></div><div> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><p class="MsoNormal" style="font-size:12.8px">Hello MAKER google group,</p><div style="font-size: 12.8px; "> <br class="webkit-block-placeholder"></div><p class="MsoNormal" style="font-size:12.8px">For the final round of a MAKER annotation for a de novo plant genome assembly, I ran MAKER twice: once with keep_preds=0 which annotated 20,284 genes and once with keep_preds=1 which annotated 34,055 genes.</p><div style="font-size: 12.8px; "> <br class="webkit-block-placeholder"></div><p class="MsoNormal" style="font-size:12.8px">I ran the 34,055 genes (the keep_preds=1 set) through InterProScan to search the MAKER predictions for protein domain content and added this IPRScan output into the MAKER gff file with <font face="arial, helvetica, sans-serif">the ipr_update_gff accessory script.</font></p><div style="font-size: 12.8px; "><font face="arial, helvetica, sans-serif"> </font><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="font-size:12.8px"><font face="arial, helvetica, sans-serif">The game plan is to go through the 34,055 genes and remove any gene model that doesn’t have either protein domain content or physical evidence. I</font> am counting genes that have an AED=1 as the genes that don’t have physical evidence.</p><div style="font-size: 12.8px; "> <br class="webkit-block-placeholder"></div><p class="MsoNormal" style="font-size:12.8px">I have two questions: </p><p class="MsoNormal" style="font-size:12.8px"><br></p><p class="MsoNormal" style="font-size:12.8px">1. I count 11,762 genes that have AED=1.0 in the keep_preds=1 annotation set, which leaves me with 22,293 genes that I’m assuming have some physical evidence (34,055-11,762=22,293). But when I ran MAKER with keep_preds=0 originally, I only count 20,284 genes. What are the extra ~2,000 genes that are being annotated in the keep_preds=1 run that have and AED score of less than 1.0, but are not being annotated in the keep_preds=0 run?</p><div style="font-size: 12.8px; "> <br class="webkit-block-placeholder"></div><p class="MsoNormal" style="font-size:12.8px">2. My second question is if there is an accessory script available that will remove genes that lack either the IPRScan protein domains or physical evidence <span style="font-size:10pt;font-family:arial;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">(AED < 1)</span>? This type of gene removal was mentioned in a previous post from 2012 (<a href="https://groups.google.com/forum/#!searchin/maker-devel/sorry$20there$27s$20not$20a$20script$20prepackaged$20with$20MAKER$20for$20that$20yet.%7Csort:relevance/maker-devel/VaoXWlGHOjs/EElr_otrK8QJ" target="_blank">https://groups.google.com/<wbr>forum/#!searchin/maker-devel/<wbr>sorry$20there$27s$20not$20a$<wbr>20script$20prepackaged$20with$<wbr>20MAKER$20for$20that$20yet.%<wbr>7Csort:relevance/maker-devel/<wbr>VaoXWlGHOjs/EElr_otrK8QJ</a>) and I was just wondering if since then someone wrote a script that will do this for me.</p><p class="MsoNormal" style="font-size:12.8px"><br></p><p class="MsoNormal" style="font-size:12.8px">If anyone could offer me any feedback, that would be greatly appreciated! </p><p class="MsoNormal" style="font-size:12.8px"><br></p><p class="MsoNormal" style="font-size:12.8px">Thank you,</p><p class="MsoNormal" style="font-size:12.8px"><br></p><p class="MsoNormal" style="font-size:12.8px">Allison</p><div class="gmail-yj6qo gmail-ajU" style="margin:2px 0px 0px;font-size:12.8px"></div></div>
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