{"id":996,"date":"2020-11-09T16:16:48","date_gmt":"2020-11-09T15:16:48","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=996"},"modified":"2022-04-06T14:48:56","modified_gmt":"2022-04-06T12:48:56","slug":"996-2","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-galaxy\/996-2\/","title":{"rendered":"Trainings 2019 &#8211; Galaxy Practice"},"content":{"rendered":"<h2>Galaxy Practice<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Hands On Lab Exercises for Galaxy<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Related-course materials<\/td>\n<td style=\"text-align: left;\"><a href=\"http:\/\/galaxyproject.github.io\/training-material\/topics\/introduction\/slides\/introduction.html#22\">Galaxy introduction<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">Alexis Dereeper (alexis.dereeper@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">15\/03\/2018<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">15\/03\/2018<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Summary<\/h3>\n<ul>\n<li><a href=\"#practice-1\">Practice 1: Basics of Galaxy (by Galaxy team)<\/a><\/li>\n<li><a href=\"#practice-2\">Practice 2: How to import datasets<\/a><\/li>\n<li><a href=\"#practice-3\">Practice 3: Concrete application: from reads to SNPs<\/a><\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-1\"><\/a><\/p>\n<h3>Practice 1 : Basics of Galaxy (by Galaxy team)<\/h3>\n<p>Practice1 will be performed in the <a href=\"https:\/\/usegalaxy.org\/\">Galaxy main<\/a> -<br \/>\nPractice1 consists of following the <a href=\"http:\/\/galaxyproject.github.io\/training-material\/topics\/introduction\/tutorials\/galaxy-intro-101\/tutorial.html#find-exons-with-the-highest-number-of-snps\">&quot;Galaxy 101&quot; hands-on provided by Galaxy team<\/a><\/p>\n<hr \/>\n<p><a name=\"practice-1\"><\/a><\/p>\n<h3>Practice 2 : How to import datasets<\/h3>\n<p>Practice2 will be performed in the Galaxy South Green. <\/p>\n<ul>\n<li>Connect to <a href=\"http:\/\/galaxy.southgreen.fr\/galaxy\/\">Galaxy South Green<\/a> -<\/li>\n<li>Log in using FormationN@cirad.fr account<\/li>\n<li>Rename your history &quot;test data upload&quot;<\/li>\n<\/ul>\n<p>Test the different ways to import datasets into your history:<\/p>\n<ul>\n<li>Copy\/paste the content of a dataset<\/li>\n<li>Copy\/paste the link\/URL of an external file to be imported - <code>http:\/\/rice.plantbiology.msu.edu\/pub\/data\/Eukaryotic_Projects\/o_sativa\/annotation_dbs\/pseudomolecules\/mitochondrion.dir\/chrM.cds<\/code><\/li>\n<li>Upload any txt file from your local computer<\/li>\n<li>Use FTP procedure to upload big file following the <a href=\"http:\/\/galaxy.southgreen.fr\/galaxy\/u\/dereeper\/p\/howtoload\">procedure<\/a> described form Galaxy homepage<\/li>\n<li>Import a dataset from a shared data library<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-3\"><\/a><\/p>\n<h3>Practice 3 : Concrete application: From reads to SNPs<\/h3>\n<p>Practice3 will be performed in the Galaxy South Green.<\/p>\n<ul>\n<li>Create a new history for this practice (ex: SNP calling)<\/li>\n<li>From <code>Shared data =&gt; Data libraries<\/code>, import into your history fastq datasets for 3 individuals (RC1, RC2, RC3) as well as reference fasta<br \/>\n<code>Galaxy_trainings_2015 =&gt; NGS<\/code><\/li>\n<li>Check these 6 files and create a collection of 3 dataset pairs <code>Build a list of dataset pairs<\/code>. Associate files by pair and give a name to your collection<\/li>\n<li>Process a FastqC analysis for RC1 to control the quality of sequencing<\/li>\n<li>Import the shared workflow called <code>Mapping_SNPCalling_PairedEnd<\/code><\/li>\n<li>Observe the different steps of the workflow<\/li>\n<li>Run the complete workflow. It provides a collection of Bam files.<\/li>\n<li>Observe the final VCF output<\/li>\n<\/ul>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li><a target=\"_blank\" href=\"http:\/\/galaxyproject.github.io\/training-material\/topics\/introduction\/slides\/introduction.html#1\" rel=\"noopener noreferrer\">Related courses: Galaxy introduction<\/a><\/li>\n<li><a target=\"_blank\" href=\"https:\/\/usegalaxy.org\/\" rel=\"noopener noreferrer\">Galaxy main<\/a><\/li>\n<li><a target=\"_blank\" href=\"http:\/\/bioinfo-inter.ird.fr:8080\/\" rel=\"noopener noreferrer\">Galaxy IRD<\/a><\/li>\n<li><a target=\"_blank\" href=\"http:\/\/galaxy.southgreen.fr\/galaxy\/\" rel=\"noopener noreferrer\">Galaxy CIRAD<\/a><\/li>\n<li><a target=\"_blank\" href=\"https:\/\/galaxyproject.github.io\/training-material\/\" rel=\"noopener noreferrer\">Galaxy trainings materials<\/a><\/li>\n<\/ul>\n<hr \/>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Galaxy Practice Description Hands On Lab Exercises for Galaxy Related-course materials Galaxy introduction Authors Alexis Dereeper (alexis.dereeper@ird.fr) Creation Date 15\/03\/2018&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-galaxy\/996-2\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":975,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-996","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Trainings 2019 - Galaxy Practice - itrop<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-galaxy\/996-2\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Trainings 2019 - Galaxy Practice - itrop\" \/>\n<meta property=\"og:description\" content=\"Galaxy Practice Description Hands On Lab Exercises for Galaxy Related-course materials Galaxy introduction Authors Alexis Dereeper (alexis.dereeper@ird.fr) Creation Date 15\/03\/2018&hellip; 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