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| 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 | ||
| --- | ||
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| <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> | ||
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| <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> | ||
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| <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> | ||
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| ### 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> | ||
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| <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> | ||
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| <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> | ||
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| <div id="nextInline" class="clearfix"> | ||
| <h3>Instructors</h3> | ||
| <ul> | ||
| <li>Alexis Dereeper (AD) - [email protected] </li> | ||
| <li>Camilo Ernesto Lopez (Universidad Nacional de Colombia (UNAL))</li> | ||
| </ul> | ||
| <hr/> | ||
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| </div> | ||
| </div> | ||
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