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lesson
Marc Galland, Tijs Bliek, Ken Kraaijeveld
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Welcome!

This lesson will introduce you to the basics of gene expression analysis using RNA-Seq (short for RNA sequencing). Due to the considerable progress and constant decreasing costs of RNA-Seq, this technique has became a standard technique in biology.

It is going to be fun and empowering! You will discover how total RNA are converted to short sequences called "reads" that can in turn be used to get insights into gene expression. Through careful experimental design, these gene expression information can yield new research avenues and answer crucial questions.

We will use mostly R and its companion RStudio to perform our RNA-Seq analyses and visualisations.

Depending on the level of participants, the bioinformatic part might be performed (QC of fastq files, genome alignment, counting, etc.). For this, we will use a Docker image containing all necessary datasets and softwares.

Before you begin, be sure you are all set up (see below). For complete information, see the Setup section.

Main learning objectives

After completing this lesson, you should be able to:

  • Indicate the reasons for doing an RNA-Seq experiment.
  • Identify good practices when designing a RNA-Seq experiment.
  • Memorize the steps of a complete RNA-Seq experiment: from sequencing to analysis.
  • Assess the quality of RNA-seq sequencing data ("reads") using the command-line instructions in the cloud (Linux).
  • Align RNA-seq reads to a reference genome using a splice-aware aligner (e.g. STAR).
  • Generate a count matrix from the RNA-seq data alignment
  • Perform a QC of your experiment through Principal Component Analysis (PCA) and sample clustering.
  • Execute a differential gene expression analysis using R and the DESeq2 package.
  • Be able to create key plots: volcano plot, heatmap and clustering of differentially expressed genes.
  • Provide a biological interpretation to differentially expressed genes through ORA/GSEA analyses and data integration.

Before you start

Before the training, please make sure you have done the following:

  1. Consult what you need to do in the lesson Setup.
  2. Read the workshop Code of Conduct to make sure this workshop stays welcoming for everybody.
  3. Get comfortable: if you're not in a physical workshop, get two screens if possible. You will be following along in RStudio on your own computer while also following this tutorial on your own. More instructions are available on the workshop website in the Setup section. {: .prereq}

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Citation

If you make use of this material in some way (teaching, vocational training, research), please cite us: "Bliek Tijs, Frans van der Kloet and Marc Galland" (eds): "RNA-seq lesson." Version 2020.04. https://github.com/ScienceParkStudyGroup/rnaseq-lesson

Credits

This lesson is heavily based on teaching materials from the Harvard Chan Bioinformatics Core (HBC) in-depth NGS data analysis course. Materials have been adapted and some exercises created to comply with the Carpentries Foundation teaching requirements.