<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;">Thank you Carson for your quick response. Sorry, I have another question concerning Augustus Training. You posted previously in the mailing list a link to an explanation of Augustus training steps </span><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;"><a href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html" style="cursor: pointer; font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; text-align: start; widows: 2; -webkit-text-stroke-width: 0px; word-spacing: 0px;" data-mce-href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html" data-mce-style="cursor: pointer; font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; text-align: start; widows: 2; -webkit-text-stroke-width: 0px; word-spacing: 0px;"><span style="color: #7030a0; border: none windowtext 1.0pt; padding: 0cm; background: white; text-decoration: none; text-underline: none;" data-mce-style="color: #7030a0; border: none windowtext 1.0pt; padding: 0cm; background: white; text-decoration: none; text-underline: none;">http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.htm</span></a></span><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;">l</span><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;">. Unfortunately the link doesn't work anymore. Otherwise could you explain how to filter the gff file produced by the first run of Maker to get best full length ORF as a set of gene models to train Augustus ?</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;"><br data-mce-bogus="1"></span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;">Best,</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;">Amine</span></p></div><div><br></div><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>De: </b>"chebbi mohamed amine" <mohamed.amine.chebbi@univ-poitiers.fr><br><b>À: </b>"Carson Holt" <carsonhh@gmail.com><br><b>Cc: </b>maker-devel@yandell-lab.org<br><b>Envoyé: </b>Mercredi 12 Octobre 2016 11:44:21<br><b>Objet: </b>Re: [maker-devel] Combining and merging two Maker annotation gff files ?<br></div><div><br></div><div data-marker="__QUOTED_TEXT__"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;" data-mce-style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000;"><div><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;">Thank you Carson for your quick response. Sorry, I have another question concerning Augustus Training. You posted previously in the mailing list a link to an explanation of Augustus training steps </span><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;"><a href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html" style="cursor: pointer; font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; text-align: start; widows: 2; -webkit-text-stroke-width: 0px; word-spacing: 0px;" target="_blank" data-mce-href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html" data-mce-style="cursor: pointer; font-variant-ligatures: normal; font-variant-caps: normal; orphans: 2; text-align: start; widows: 2; -webkit-text-stroke-width: 0px; word-spacing: 0px;"><span style="color: #7030a0; border: none windowtext 1.0pt; padding: 0cm; background: white; text-decoration: none; text-underline: none;" data-mce-style="color: #7030a0; border: none windowtext 1.0pt; padding: 0cm; background: white; text-decoration: none; text-underline: none;">http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.htm</span></a></span><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; color: #7030a0;">l</span><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;">. Unfortunately the link doesn't work anymore. Otherwise could you explain how to filter the gff file produced by the first run of Maker to get best full length ORF as a set of gene models to train Augustus ?</span></p><p style="margin: 0px;" data-mce-style="margin: 0px;"><span style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;" data-mce-style="font-size: 12.0pt; line-height: 115%; font-family: 'Times New Roman','serif'; background: white;"><br></span></p></div><br><hr id="zwchr"><div><b>De: </b>"Carson Holt" <carsonhh@gmail.com><br><b>À: </b>"Mohamed Amine CHEBBI" <mohamed.amine.chebbi@univ-poitiers.fr><br><b>Cc: </b>maker-devel@yandell-lab.org<br><b>Envoyé: </b>Mardi 11 Octobre 2016 22:05:50<br><b>Objet: </b>Re: [maker-devel] Combining and merging two Maker annotation gff files ?<br></div><br><div>Masking doesn’t just affect the gene models, but also evidence alignment and thus scoring. So merging in this way would not make much sense as the second less masked set would always score better because it has more evidence alignments permitted by the lack of masking (not necessarily real, but drawn in by repeats).<div class=""><br class=""></div><div class="">The result would be that any attempt of a merge would almost exclusively result in all genes from the second set always scoring higher.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote class=""><div class="">On Oct 10, 2016, at 3:43 AM, Mohamed Amine CHEBBI <<a href="mailto:mohamed.amine.chebbi@univ-poitiers.fr" class="" target="_blank" data-mce-href="mailto:mohamed.amine.chebbi@univ-poitiers.fr">mohamed.amine.chebbi@univ-poitiers.fr</a>> wrote:</div><div class=""><p class="MsoNormal" style="margin: 0cm 0cm 10pt; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;" data-mce-style="margin: 0cm 0cm 10pt; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;"><span lang="EN-US" style="font-size: 12pt; color: #222222; background-color: white; background-position: initial initial; background-repeat: initial initial;" class="" data-mce-style="font-size: 12pt; color: #222222; background-color: white; background-position: initial initial; background-repeat: initial initial;">Hi!<span class="Apple-converted-space"> </span><br class=""><br class="">I’m using the latest version of Maker2 to annotate an arthropod genome. First, I have run RepeatModeler to create rmlib for Maker, then I have followed two independent annotation strategies on the same assembly :<br class="">1- Passing throw Maker all the repeats collected by RepeatModeler ( Identified repeats in the Repbase + Unkown Models).<br class="">2- <span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 12pt;" class="" data-mce-style="font-size: 12pt;">Passing throw Maker only the identified repeats.<span class="Apple-converted-space"> </span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 10pt; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;" data-mce-style="margin: 0cm 0cm 10pt; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;"><span lang="EN-US" style="font-size: 12pt;" class="" data-mce-style="font-size: 12pt;">Both annotations work successfully. The first annotation gives me 19048 genes against 22931 done by the second one. Know, I'm seeing for a mean to merge the two annotation gff files without<span class="Apple-converted-space"> </span><span style="text-decoration: underline;" data-mce-style="text-decoration: underline;">doing a re-annotation<span class="Apple-converted-space"> </span></span>and by taking the best and non redundant supported gene models .</span></p><p class="MsoNormal" style="margin: 0cm 0cm 10pt; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;" data-mce-style="margin: 0cm 0cm 10pt; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;"><span lang="EN-US" style="font-size: 12pt;" class="" data-mce-style="font-size: 12pt;">So, do you think that configuring the maker options as below, could resolve this issue :<br class="">maker_gff=1-mask-all.gff,2-mask-onlyKnown.gff #MAKER derived GFF3 file<br class="">#MAKER derived GFF3 file<br class="">est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no<br class="">altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no<br class="">protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no<br class="">rm_pass=1 #use repeats in maker_gff: 1 = yes, 0 = no<br class="">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no<br class="">pred_pass=1 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no<br class="">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</span></p><span lang="EN-US" style="font-family: Helvetica; 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font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;"></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;"></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;"></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;"></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;"></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;"></span><pre class="moz-signature" style="font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff;" data-mce-style="font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: #ffffff;">--
Mohamed Amine CHEBBI, PhD Student
Université de Poitiers
</pre><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff;"><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: 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: #ffffff; float: none; display: inline !important;" class="" data-mce-style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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