{"id":1238,"date":"2016-07-12T11:39:49","date_gmt":"2016-07-12T09:39:49","guid":{"rendered":"http:\/\/vm-bioinfo-wp.toulouse.inra.fr\/?page_id=1238"},"modified":"2022-03-08T16:19:09","modified_gmt":"2022-03-08T15:19:09","slug":"rnaseq-bioinfobiostats","status":"publish","type":"page","link":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/","title":{"rendered":"RNAseq bioinfo\/biostats"},"content":{"rendered":"<h6 class=\"csc-firstHeader\">Introduction<\/h6>\n<p>This page contains the material (files, links,&#8230;) used during the RNA-Seq course given by the MIAT Unit and Bioinfo Genotoul platform.<\/p>\n<p>It also contains some Genotoul scripts for biostatistics.<\/p>\n<h6>Slides and exercises<\/h6>\n<ul>\n<li>Command line slides and exercises <a href=\"http:\/\/genoweb.toulouse.inra.fr\/~formation\/19_Rnaseq_Cli\/doc\">see<\/a><\/li>\n<li>Galaxy slides and exercises <a href=\"http:\/\/genoweb.toulouse.inra.fr\/~formation\/4_Galaxy_RNAseq\/\">go<\/a><\/li>\n<li>Data for training, are available in previous links under data directory.<\/li>\n<\/ul>\n<p>Lots of\u00a0 informations about RNAseq statistic analysis are available <a href=\"http:\/\/www.nathalievialaneix.eu\/teaching\/rnaseq.html\">here<\/a><\/p>\n<h6>Biostatistics scripts on genotoul<\/h6>\n<p>More info about scripts presented in this page are available here: <a href=\"http:\/\/genoweb.toulouse.inra.fr\/~formation\/LigneCmd\/RNAseq\/doc\/RScriptsDocumentation.pdf\">genoweb.toulouse.inra.fr\/~formation\/LigneCmd\/RNAseq\/doc\/RScriptsDocumentation.pdf<\/a><\/p>\n<div id=\"c346\" class=\"csc-default\">\n<div class=\"csc-header csc-header-n2\">\n<h6>Input data<\/h6>\n<\/div>\n<p class=\"bodytext\">Format your count table like this (separator tabulation)<\/p>\n<pre>gene_id\u00a0\u00a0 \u00a0untreated1\u00a0\u00a0 \u00a0untreated2\u00a0\u00a0 \u00a0untreated3\u00a0\u00a0 \u00a0untreated4\u00a0\u00a0 \u00a0treated1\u00a0\u00a0 \u00a0treated2\u00a0\u00a0 \u00a0treated3 \r\nFBgn0000003\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a01 \r\nFBgn0000008\u00a0\u00a0 \u00a092\u00a0\u00a0 \u00a0161\u00a0\u00a0 \u00a076\u00a0\u00a0 \u00a070\u00a0\u00a0 \u00a0140\u00a0\u00a0 \u00a088\u00a0\u00a0 \u00a070 \r\nFBgn0000014\u00a0\u00a0 \u00a05\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a04\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00 \r\nFBgn0000015\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a02\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a02\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00 \r\nFBgn0000017\u00a0\u00a0 \u00a04664\u00a0\u00a0 \u00a08714\u00a0\u00a0 \u00a03564\u00a0\u00a0 \u00a03150\u00a0\u00a0 \u00a06205\u00a0\u00a0 \u00a03072\u00a0\u00a0 \u00a03334 \r\nFBgn0000018\u00a0\u00a0 \u00a0583\u00a0\u00a0 \u00a0761\u00a0\u00a0 \u00a0245\u00a0\u00a0 \u00a0310\u00a0\u00a0 \u00a0722\u00a0\u00a0 \u00a0299\u00a0\u00a0 \u00a0308 \r\nFBgn0000022\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00 \r\nFBgn0000024\u00a0\u00a0 \u00a010\u00a0\u00a0 \u00a011\u00a0\u00a0 \u00a03\u00a0\u00a0 \u00a03\u00a0\u00a0 \u00a010\u00a0\u00a0 \u00a07\u00a0\u00a0 \u00a05 \r\nFBgn0000028\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a01 \r\nFBgn0000032\u00a0\u00a0 \u00a01446\u00a0\u00a0 \u00a01713\u00a0\u00a0 \u00a0615\u00a0\u00a0 \u00a0672\u00a0\u00a0 \u00a01698\u00a0\u00a0 \u00a0696\u00a0\u00a0 \u00a0757 \r\nFBgn0000036\u00a0\u00a0 \u00a02\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a01\u00a0\u00a0 \u00a00\u00a0\u00a0 \u00a01 \r\nFBgn0000037\u00a0\u00a0 \u00a015\u00a0\u00a0 \u00a025\u00a0\u00a0 \u00a09\u00a0\u00a0 \u00a05\u00a0\u00a0 \u00a020\u00a0\u00a0 \u00a014\u00a0\u00a0 \u00a017<\/pre>\n<p class=\"bodytext\">Test data are available here : <a href=\"http:\/\/www.nathalievialaneix.eu\/doc\/gz\/RNAseq_data.tar.gz\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/www.nathalievialaneix.eu\/doc\/gz\/RNAseq_data.tar.gz<\/a><\/p>\n<p><code>wget http:\/\/www.nathalievialaneix.eu\/doc\/gz\/RNAseq_data.tar.gz<\/code><\/p>\n<p><code>tar -xvzf RNAseq_data.tar.gz<\/code><\/p>\n<\/div>\n<div id=\"c348\" class=\"csc-default\">\n<div class=\"csc-header csc-header-n3\">\n<h6>Fix R environment variable for cluster<\/h6>\n<\/div>\n<ul class=\"prettylist\">\n<li>go on a node:<br \/>\n<code>srun -c 4 --pty bash<\/code><\/li>\n<li>Fix your environment variable:<br \/>\n<code>export R_LIBS=\"~\/work\/Rlib\"<\/code><br \/>\n<code>mkdir ~\/work\/Rlib<\/code><\/li>\n<li>Load R module :<br \/>\n<code>module load system\/R-3.5.1<\/code><\/li>\n<\/ul>\n<\/div>\n<div id=\"c347\" class=\"csc-default\">\n<div class=\"csc-header csc-header-n4\">\n<h6>Run normalization<\/h6>\n<\/div>\n<ul class=\"prettylist\">\n<li>Get help:<br \/>\n<code>Rscript \/usr\/local\/bioinfo\/Scripts\/bin\/Normalization.R<\/code><\/li>\n<li>Run:<br \/>\n<code>Rscript \/usr\/local\/bioinfo\/Scripts\/bin\/Normalization.R -f count_table.tsv -o .\/normalization<\/code><\/li>\n<li>List result directory:<br \/>\nls .\/normalization<\/li>\n<li>Download image and pdf in local machine to view:<br \/>\n<code>scp user@genologin.toulouse.inra.fr:~\/work\/normalization .<\/code><\/li>\n<li>Select the normalization where boxplots and density plot are best aligned and where libraries are well separate in PCA.<\/li>\n<\/ul>\n<\/div>\n<div id=\"c349\" class=\"csc-default\">\n<div class=\"csc-header csc-header-n5\">\n<h6>Run differential expression detection<\/h6>\n<\/div>\n<ul class=\"prettylist\">\n<li>Get help:<br \/>\n<code>Rscript \/usr\/local\/bioinfo\/Scripts\/bin\/DEG.R<\/code><\/li>\n<li>Run script ( with initial matrix and normalization info file):<br \/>\n<code>Rscript \/usr\/local\/bioinfo\/Scripts\/bin\/DEG.R -f count_table.tsv -n .\/normalization\/RLE_info.txt -o DEG --pool1 untreated1,untreated2,untreated3,untreated4 --pool2=treated1,treated2,treated3 --filter TRUE --alpha 0.05 --correct BH --MAplots TRUE<\/code><\/li>\n<li>Download result on your computer<br \/>\n<code>scp user@genotoul.toulouse.inra.fr:~\/work\/DEG .<\/code><\/li>\n<li>Your differential expressed genes are available in :<br \/>\nDEG\/resDEG.csv<\/li>\n<\/ul>\n<\/div>\n<div id=\"c350\" class=\"csc-default\">\n<div class=\"csc-header csc-header-n6\">\n<h6>Perform GO enrichment<\/h6>\n<\/div>\n<ul class=\"prettylist\">\n<li>Get help:<br \/>\n<code>Rscript \/usr\/local\/bioinfo\/Scripts\/bin\/GOEnrichment.R<\/code><\/li>\n<li>If your are working with the example matrix ( count_table.tsv of flybase) download GO from flybase <a href=\"ftp:\/\/ftp.flybase.net\/releases\/current\/precomputed_files\/go\/gene_association.fb.gz\" target=\"_blank\" rel=\"noopener noreferrer\">ftp:\/\/ftp.flybase.net\/releases\/current\/precomputed_files\/go\/gene_association.fb.gz<\/a><br \/>\n<code>wget <a href=\"ftp:\/\/ftp.flybase.net\/releases\/current\/precomputed_files\/go\/gene_association.fb.gz\" target=\"_blank\" rel=\"noopener noreferrer\">ftp:\/\/ftp.flybase.net\/releases\/current\/precomputed_files\/go\/gene_association.fb.gz<\/a><\/code><br \/>\n<code>gunzip <a href=\"ftp:\/\/ftp.flybase.net\/releases\/current\/precomputed_files\/go\/gene_association.fb.gz\" target=\"_blank\" rel=\"noopener noreferrer\">gene_association.fb.gz<\/a><\/code><\/li>\n<li>generate expected 2 columns format :<br \/>\n<code>grep -v '^!' gene_association.fb | cut -f 2,5 &gt; fb.go<\/code><\/li>\n<li>Run Go enrichment on resDEG.csv :<br \/>\n<code>Rscript \/usr\/local\/bioinfo\/Scripts\/bin\/GOEnrichment.R -f fb.go --fileFormat twoColumns -i DEG\/resDEG.csv -o GOEnrichment -a classic -t fisher<\/code><\/li>\n<li>Download result on your computer :<br \/>\n<code>scp user@genologin.toulouse.inra.fr:~\/work\/GOEnrichment .<\/code><\/li>\n<\/ul>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Introduction This page contains the material (files, links,&#8230;) used during the RNA-Seq course given by the MIAT Unit and Bioinfo Genotoul platform. It also contains some Genotoul scripts for biostatistics. Slides and exercises Command&#46;&#46;&#46;<\/p>\n","protected":false},"author":7,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v20.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>RNAseq bioinfo\/biostats - genotoul-bioinfo<\/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.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"RNAseq bioinfo\/biostats - genotoul-bioinfo\" \/>\n<meta property=\"og:description\" content=\"Introduction This page contains the material (files, links,&#8230;) used during the RNA-Seq course given by the MIAT Unit and Bioinfo Genotoul platform. It also contains some Genotoul scripts for biostatistics. Slides and exercises Command&#046;&#046;&#046;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/\" \/>\n<meta property=\"og:site_name\" content=\"genotoul-bioinfo\" \/>\n<meta property=\"article:modified_time\" content=\"2022-03-08T15:19:09+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/\",\"url\":\"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/\",\"name\":\"RNAseq bioinfo\/biostats - genotoul-bioinfo\",\"isPartOf\":{\"@id\":\"https:\/\/bioinfo.genotoul.fr\/#website\"},\"datePublished\":\"2016-07-12T09:39:49+00:00\",\"dateModified\":\"2022-03-08T15:19:09+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/bioinfo.genotoul.fr\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"RNAseq bioinfo\/biostats\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/bioinfo.genotoul.fr\/#website\",\"url\":\"https:\/\/bioinfo.genotoul.fr\/\",\"name\":\"genotoul-bioinfo\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/bioinfo.genotoul.fr\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/bioinfo.genotoul.fr\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/bioinfo.genotoul.fr\/#organization\",\"name\":\"genotoul-bioinfo\",\"url\":\"https:\/\/bioinfo.genotoul.fr\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/bioinfo.genotoul.fr\/#\/schema\/logo\/image\/\",\"url\":\"\",\"contentUrl\":\"\",\"caption\":\"genotoul-bioinfo\"},\"image\":{\"@id\":\"https:\/\/bioinfo.genotoul.fr\/#\/schema\/logo\/image\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"RNAseq bioinfo\/biostats - genotoul-bioinfo","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/","og_locale":"en_US","og_type":"article","og_title":"RNAseq bioinfo\/biostats - genotoul-bioinfo","og_description":"Introduction This page contains the material (files, links,&#8230;) used during the RNA-Seq course given by the MIAT Unit and Bioinfo Genotoul platform. It also contains some Genotoul scripts for biostatistics. Slides and exercises Command&#46;&#46;&#46;","og_url":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/","og_site_name":"genotoul-bioinfo","article_modified_time":"2022-03-08T15:19:09+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/","url":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/","name":"RNAseq bioinfo\/biostats - genotoul-bioinfo","isPartOf":{"@id":"https:\/\/bioinfo.genotoul.fr\/#website"},"datePublished":"2016-07-12T09:39:49+00:00","dateModified":"2022-03-08T15:19:09+00:00","breadcrumb":{"@id":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/bioinfo.genotoul.fr\/index.php\/rnaseq-bioinfobiostats\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/bioinfo.genotoul.fr\/"},{"@type":"ListItem","position":2,"name":"RNAseq bioinfo\/biostats"}]},{"@type":"WebSite","@id":"https:\/\/bioinfo.genotoul.fr\/#website","url":"https:\/\/bioinfo.genotoul.fr\/","name":"genotoul-bioinfo","description":"","publisher":{"@id":"https:\/\/bioinfo.genotoul.fr\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/bioinfo.genotoul.fr\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/bioinfo.genotoul.fr\/#organization","name":"genotoul-bioinfo","url":"https:\/\/bioinfo.genotoul.fr\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/bioinfo.genotoul.fr\/#\/schema\/logo\/image\/","url":"","contentUrl":"","caption":"genotoul-bioinfo"},"image":{"@id":"https:\/\/bioinfo.genotoul.fr\/#\/schema\/logo\/image\/"}}]}},"_links":{"self":[{"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/pages\/1238"}],"collection":[{"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/comments?post=1238"}],"version-history":[{"count":9,"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/pages\/1238\/revisions"}],"predecessor-version":[{"id":19194,"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/pages\/1238\/revisions\/19194"}],"wp:attachment":[{"href":"https:\/\/bioinfo.genotoul.fr\/index.php\/wp-json\/wp\/v2\/media?parent=1238"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}