<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi, </div><div class=""><br class=""></div><div class="">Thank you for your reply, nevertheless it doesn't it answer my question. Either I didn't express myself well enough or I don't get something obvious from your answer.</div><div class=""><br class=""></div><div class="">I will try to rephrase the problem.</div>My problem is that I am setting keep_phred=0 and that I obtain AED of 1. Can unsupported data can be selected with keep_phred=0? what I understood is that it is not the case so do you have any idea of why I have those AED equal to 1?<div class=""><br class=""></div><div class="">Thank you again for your help.</div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Jacques<br class=""><div class="">
<div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div></div>
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<div><br class=""><blockquote type="cite" class=""><div class="">On 4 May 2018, at 20:30, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">By default MAKER will not let models through without at least some degree of evidence overlap (AED < 1). This is because ab initio predictors overcall (sometimes by as much as a factor of 10, i.e. 10 false positives for every true positive). You can dial in the minimum AED support using the AED_threshold. But if yo8u want to keep everything that does not have overlap with a better supported model then setting keep_pred=1 will allow even unsupported models to be maintained (1 for yes and 0 for no). Situations where you may want to do this include passing in old annotation datasets or working on organisms with very high genedensity and low ab initio false positive rates (many species of fungi meet this criteria).<br class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On May 2, 2018, at 5:55 AM, Jacques Dainat <<a href="mailto:jacques.dainat@nbis.se" class="">jacques.dainat@nbis.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">It is not the first time I see that, but I have an annotation launched with the option keeps_pred=0 that contains gene models with AED score equal to 1. As far as I understand, AED score to 1 means there is no evidence support. So it should be purely abinitio without any line of evidence in front of this prediction.</div><div class="">But as it is written in “Michael S-Cambell et <i class="">al.</i>, Genome Annotation and Curation Using MAKER and MAKER-P, Current Protocols in Bioinformatics, 2014” page 4.11.36 about the the keep_preds option:</div><div class=""><b class="">"MAKER rejects models that do not have at least some form of evidence support.” </b>Setting<b class=""> </b>keep_preds to 1 “remove the evidence support requirement”.</div><div class=""><br class=""></div><div class="">So, how should I understand my results? Some predictions with low support (but support anyway) can have AED score equal to 1? Or some purely abinitio prediction without support at all can anyway be selected even when keep_preds=0 is set up? </div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">Jacques Dainat<br class="">
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