<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;" class="">Hi Patrick,<div class=""><br class=""></div><div class="">For point 1, the best AED cutoff to use is quite arbitrary. For one the last genomes that I annotated we had a set of high quality genes identified based on synteny with genes in closely related genomes. We plotted the distribution of AEDs for those genes and found that a cutoff of 0.28 captured 98% of the high quality genes. This value would vary based on the evidence provided. I’ve used 0.5 in the past as a more permissive filter.</div><div class=""><br class=""></div><div class="">For point 2, these is a accessory script in the MAKER bin called quality_filter.pl. It has an option (-a) that allows you to put in an AED cutoff and it will filter the gff3 file based on that cutoff.</div><div class=""><br class=""></div><div class="">For general processing of GFF3 files, there is a perl library called GAL that is useful if you write code in perl.</div><div class=""><br class=""></div><div class="">Take care,</div><div class="">Mike</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 19, 2017, at 9:11 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span itemscope="" itemtype="http://schema.org/Question" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span itemprop="text" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi,</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I have successfully annotated my genome with MAKER. Now I have a gff file that I want to post process /filter.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">In particular, I would like to discard genes that are below to a certain AED score.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">1) Is there an AED treshold from where a gene is not strongly supported ? if yes, do you have some reference about this ?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">2) Is there a script/software to process a gff file ?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks</div></span></span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class=""></span><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div id="Signature" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class=""><br class="">Patrick Tran Van<br class=""><br class="">Groups Chapuisat, Robinson-Rechavi & Schwander<br class="">Department of Ecology and Evolution<br class="">University of Lausanne<br class="">Le Biophore<br class="">CH-1015 Lausanne<br class="">Switzerland<br class="">Office 3206<br class=""><br class=""></div></div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; 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