{"id":1067,"date":"2020-11-10T16:07:32","date_gmt":"2020-11-10T15:07:32","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=1067"},"modified":"2022-04-06T14:50:08","modified_gmt":"2022-04-06T12:50:08","slug":"trainings-2019-trinity","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-trinity\/","title":{"rendered":"Trainings 2019 &#8211; Trinity"},"content":{"rendered":"<h2>Trinity-Trinotate<\/h2>\n<table class=\"table-contact\">\n<tr>\n<td width=\"15%\"><img decoding=\"async\" width=\"200%\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/TrinotateLogo.png\" alt=\"\" \/>\n<\/td>\n<td>\n<h1> Assembling and functionally annotating a de-novo transcriptome from RNA-seq data <\/h1>\n<p>\nThis course offers an introduction to pre-processing, assembling and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms.\n<\/td>\n<\/tr>\n<\/table>\n<h3>Prerequisites<\/h3>\n<p><a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-linux-for-dummies\/\">Linux<\/a><br \/>\n<a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-linux-for-jedi\/\">LinuxJedi<\/a><br \/>\n<a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-hpc\/\">HPC<\/a><br \/>\n<a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-rnaseq\/\">RNAseq<\/a>  <\/p>\n<div id=\"colonne1\">\n<h3>Program<\/h3>\n<ul>\n<li> Transcrits assembly with Trinity  <\/li>\n<li> Checking assembly quality  <\/li>\n<li> Differential expression analysis of transcrits (DE)  <\/li>\n<li> Funtional annotation of transcrits with Trinotate <\/li>\n<li> Codants regions prediction with TransDecoder <\/li>\n<\/ul>\n<\/div>\n<div id=\"colonne2\">\n<h3>Learning objectives<\/h3>\n<ul>\n<li> Manipulate tools available for assemblies analysis <\/li>\n<li> Study differential expression by using RNAseq data without a reference genome <\/li>\n<li> Visualize diversity metrics in assemblies approaches <\/li>\n<li> Annotate transcrits to know functions of genes  <\/li>\n<\/ul>\n<\/div>\n<div id=\"colonne3\">\n<h3>Training material<\/h3>\n<ul>\n<li> [Intro] Training introduction : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/\/files\/AA-SG-ABiMS2019\/Planning_Trinity-Assemblage-Annotation_SG-ABiMS_2019.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li> [Survival] Basic commands in SLURM : <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/slurm\/\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>Reads quality slides : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/AA-SG-ABiMS2019\/RNASeq_denovo_Montpellier_092019_0_cleaning.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>[ Practice 1. ] Checking Reads Quality <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-trinity-practice\/#practice-1\" rel=\"noopener noreferrer\">see<\/a> <\/li>\n<li>Assembly slides : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/AA-SG-ABiMS2019\/RNASeq_denovo_Montpellier_092019_1_assembly.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>[ Practice 2. ] Assembling transcriptome from RNA-seq <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-trinity-practice\/#practice-2\" rel=\"noopener noreferrer\">see<\/a> <\/li>\n<li>Assesment slides : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/AA-SG-ABiMS2019\/RNASeq_denovo_Montpellier_092019_2_assesment.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>[ Practice 3. ] Assessing transcriptome assembly quality <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-trinity-practice\/#practice-3\" rel=\"noopener noreferrer\">see<\/a> <\/li>\n<li>Annotation slides : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/\/files\/AA-SG-ABiMS2019\/RNASeq_denovo_Montpellier_092019_3_annotation.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>[ Practice 5 . ] Functional annotation <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-trinity-practice-annotation\/\" rel=\"noopener noreferrer\">see<\/a> <\/li>\n<li>Differential Expression slides : <a target=\"_blank\" href=\"https:\/\/southgreenplatform.github.io\/trainings\/files\/AA-SG-ABiMS2019\/RNASeq_denovo_Montpellier_092019_4_DEG.pdf\" rel=\"noopener noreferrer\">see<\/a><\/li>\n<li>[ Practice 4.]  Differential Expression Analysis (DE) <a target=\"_blank\" href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-trinity-practice\/\/#practice-4\" rel=\"noopener noreferrer\">see<\/a> <\/li>\n<\/ul>\n<\/div>\n<div id=\"nextInline\" class=\"clearfix\">\n<h3>Instructors<\/h3>\n<ul>\n<li> Erwan Corre (EC) - corre@sb-roscoff.fr <\/li>\n<li> Julie Orjuela-Bouniol (JO) - julie.orjuela@ird.fr<\/li>\n<li> Christine Tranchant-Dubreuil (AD) - christine.tranchant@ird.fr <\/li>\n<li> Aurore Comte (AC) - aurore.comte@ird.fr<\/li>\n<li> Stephanie SIDIBE BOCS (SSB) -  stephanie.sidibe-bocs@cirad.fr <\/li>\n<li> David Lopez (DL) -  david.lopez@cirad.fr <\/li>\n<\/ul>\n<\/div>\n<h3>Trainings<\/h3>\n<table>\n<thead>\n<tr>\n<th><strong>Date<\/strong><\/th>\n<th><strong>Location<\/strong><\/th>\n<th><strong>Topics<\/strong><\/th>\n<th><strong>Participants<\/strong><\/th>\n<th><strong>Instructors<\/strong><\/th>\n<th><strong>Links<\/strong><\/th>\n<th><strong>Units<\/strong><\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>2019<\/td>\n<td>Montpellier, France<\/td>\n<td>Introduction to assembly and annotation of transcrits<\/td>\n<td>15<\/td>\n<td>EC JO CT AC SSB DL<\/td>\n<td><\/td>\n<td>SOUTHGREEN ABiMS - IFB aliance<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"<p>Trinity-Trinotate Assembling and functionally annotating a de-novo transcriptome from RNA-seq data This course offers an introduction to pre-processing, assembling and&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-trinity\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":1321,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-1067","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - 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