From c53f1d1667cb4f5bdeba143ece4ab9540a14f9c0 Mon Sep 17 00:00:00 2001
From: dereeper <alexis.dereeper@ird.fr>
Date: Wed, 7 Feb 2024 21:34:51 +0100
Subject: [PATCH] Update 2024_UNAL.md

---
 _pages/2024_UNAL.md | 82 ++++++++++++++++++++-------------------------
 1 file changed, 37 insertions(+), 45 deletions(-)

diff --git a/_pages/2024_UNAL.md b/_pages/2024_UNAL.md
index f6f58f4..59edf38 100644
--- a/_pages/2024_UNAL.md
+++ b/_pages/2024_UNAL.md
@@ -2,73 +2,65 @@
 layout: page
 title: "UNAL Colombia Training"
 permalink: /2024_UNAL/
-tags: [workflow manager, command-line, toggle, galaxy]
-description: NGS Training Page
+tags: [transcriptomics, galaxy]
+description: RNASeq with Galaxy Training Page
 ---
-
-<table class="table-contact">
-	<tr>
-		<td>
-			In the context of a collaboration between IRD and Universidad Nacional de Colombia in Bogota, a training session is organized for manipulating data within Galaxy environment, for RNASeq analysis.
-		</td>
-	<tr>
-		<td><a class="logo" href="https://unal.edu.co/"><img class="img-logo" src="{{ site.url }}/images/logo/logo-Universidad-Nacional.png" alt="" /></a></td>
-		<td><a class="logo" href="http://www.ird.fr"><img class="img-logo"   src="{{ site.url }}/images/logo_ird.png" alt="" /></a></td>
-	</tr>
-</table>
-
 <table class="table-contact">
+<tr>
+<td><img width="100%" src="{{ site.url }}/images/trainings-rnaseq.png" alt="" />
+</td>
+<td>
+<h1> Introduction to RNASeq analysis </h1><br />
+In the context of a collaboration between IRD and Universidad Nacional de Colombia in Bogota, a training session is organized to give an introduction to RNASeq analysis in the Galaxy environment. We will cover from raw reads to differential expression analysis.
+</td>
+</tr>
 	<tr>
-		<td>
-Collaboration IRD/Universidad Nacional de Colombia
-<br />
-			
-			<hr/>
-			
-			Trainings session from 8th to 9th februry 2024 at UNAL.
-			
-			</tr>
-	<tr>
-		<td>
-Comity
-		<br />
-Camilo Ernesto Lopez (Universidad Nacional de Colombia (UNAL)), Alexis Dereeper (UMR PHIM, Plateau i-trop/plateforme South green - IRD)
-		</td></tr>
-	
+<td>
+	<a class="logo" href="https://unal.edu.co/"><img class="img-logo" src="{{ site.url }}/images/logo/logo-Universidad-Nacional.png" alt="" /></a></td>
+	<td><a class="logo" href="http://www.ird.fr"><img class="img-logo"   src="{{ site.url }}/images/logo_ird.png" alt="" /></a></td>
 </table>
 
-
+### Prerequisites
+Linux for dummies
 <div id="colonne1">
-<h3>Programme</h3>
+<h3>Program</h3>
 <ul>
-<li>Introduction to Galaxy platform </li>
-<li>Introduction to RNASeq analysis</li>
+<li> Reads preprocessing </li>
+<li> Mapping RNASeq reads against an annotated reference genome with STAR </li>
+<li> Counting reads in transcrits/genes with HTSeq-count </li>
+<li> Count normalization using Diane </li>
+<li> Differential expression analysis using Diane </li>
+<li> Plots, clustering, co-expression network: degust, WGCNA </li>
 </ul>
-    <br />
 </div>
 
+<div id="colonne2">
+<h3>Learning objectives</h3>
+<ul>
+<li>Process raw reads to count matrix </li>
+<li>Think about different normalisation methods</li>
+<li>Detect differentially expressed genes</li>
+<li>Compare results between approaches</li>
+</ul>
+</div>
 
 <div id="colonne3">
 <h3>Training material</h3>
 <ul>
-   <li>Introduction to Galaxy (Slides) : <a target="_blank" href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/introduction/slides.html#1">see</a></li>
-   <li>Introduction to Gaalxy (Practice) : <a target="_blank" href="https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.html">see</a> </li>
-	 <li>Introduction to RNASeq analysis (Slides) : <a target="_blank" href="">see</a> </li>
-	<li>Introduction to RNASeq analysis in Galaxy (Practice)  : <a target="_blank" href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html">see</a> </li>
+<li>Slides : <a target="_blank" href="{{ site.url }}files/analyse_rnaseq_2023.pdf">see</a></li>
+<li>Practice : <a target="_blank" href="{{ site.url }}/linux/rnaseqPractice">see</a> </li>
+<li>DIANE Practice : <a target="_blank" href="{{ site.url }}/linux/Analyse_Count_Diane.pdf">see</a> </li>
 </ul>
 </div>
 
-
-
 <div id="nextInline" class="clearfix">
 <h3>Instructors</h3>
 <ul>
     <li>Alexis Dereeper (AD) - alexis.dereeper@ird.fr </li>
+    <li>Camilo Ernesto Lopez (Universidad Nacional de Colombia (UNAL))</li>
 </ul>
-			
-			<hr/>
-	
 
-</div> 
+</div>
+