<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Amine,<div class=""><br class=""></div><div class="">I haven’t seen that pattern in a CFD plot of AED before. Is there a possibility that the x and y axises are swiched in the plot?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Mike<br class=""><div><blockquote type="cite" class=""><div class="">On Oct 26, 2016, at 9:09 AM, Mohamed Amine Chebbi <<a href="mailto:mohamed.amine.chebbi@univ-poitiers.fr" class="">mohamed.amine.chebbi@univ-poitiers.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;" class=""><div class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222; background: white;" class="">Hi ! </span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class="">I have tried three rounds of annotation in Maker on a non model arthropod genome (1.7Gb) which is an hybrid assembly of Pacbio and illumina reads.</span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class="">As suggested in the tutorial, I ran in the first round Maker with repeat masking to generate gene models using transcript (Trinity assembly) and protein (swissprot) evidence. Then Maker models were used twice in a bootstrap fashion to retrain SNAP. </span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class="">The number of genes drops from </span><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" class="">29207 in the round 1 to 22547 in the round 2 then increases slightly to 22931 in the round 3.</span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><br class=""> <span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" class=""><span style="font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; white-space: pre-wrap; widows: 2; -webkit-text-stroke-width: 0px; float: none; word-spacing: 0px;" data-mce-style="font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; white-space: pre-wrap; widows: 2; -webkit-text-stroke-width: 0px; float: none; word-spacing: 0px;" class="">However, the AED profile (attached) don't seem to be satisfactory.</span></span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #212121; background: white;" class="">So I wonder if you could let me a good strategy to improve the annotation quality. Do you think that filtering good transcripts could improve results. If yes , which criteria should</span><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class=""> be taken into account ?</span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class="">Thank you.</span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class=""><br data-mce-bogus="1" class=""></span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class="">Best;</span></div><div style="line-height: normal; background-color: white; margin: 0px; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" data-mce-style="font-size: 12.0pt; font-family: 'Times New Roman','serif'; color: #222222;" class="">Amine</span></div></div></div></div><span id="cid:4ABC077D-04DF-4611-B0F8-E094F3C601A9@cshl.edu"><AED-Graph.pdf></span>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></body></html>