Topic outline

  • Transcriptomics Analysis: RNA-seq

    19-21 January 2022

    Streamed from Lausanne


    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss.

  • Programme

    DAY1
    9:00 - 10:30 - Introduction to RNA sequencing
    10:30 - 10:45 - Coffee Break
    10:45 - 12:30 - RNAseq analysis pipeline, part I
    12:30 - 13:30 - Lunch Break
    13:30 - 15:00 - RNAseq analysis pipeline, part II
    15:00 - 15:15 - Coffee break
    15:15 - 17:00 - Practicals

    DAY2
    9:00 - 10:30 - Differential Expression analysis
    10:30 - 10:45 - Coffee Break
    10:45 - 12:30 - Practicals
    12:30 - 13:30 - Lunch Break
    13:30 - 15:00 - Differential splicing
    15:00 - 15:15 - Coffee break
    15:15 - 17:00 – Practicals

    DAY3
    9:00 - 10:30 - Differential Expression analysis with DESEQ2
    10:30 - 10:45 - Coffee Break
    10:45 - 12:30 - Practicals
    12:30 - 13:30 - Lunch Break
    13:30 - 15:00 - Downstream analysis
    15:00 - 15:15 - Coffee break
    15:15 - 17:00 - Practicals

    • Software installation

      Please ensure that the following software are installed on your machine PRIOR to the course:
      • FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
      • QualiMap (http://qualimap.bioinfo.cipf.es/)

      • R (https://www.r-project.org, version > 4.0)
      • latest version of R Studio

      ---------------------
      Installation of R packages for Practical 1

      if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

      BiocManager::install("NOISeq")
      BiocManager::install("Repitools")
      BiocManager::install("Rsamtools")
      BiocManager::install("Rsubread")
      BiocManager::install("rtracklayer")

      ---------------------
      Installation of R packages for Practical 2

      install.packages("devtools")
      install.packages("ggplot2")
      install.packages("gridExtra")
      install.packages("RColorBrewer")
      install.packages("reshape2")

      if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

      BiocManager::install("DESeq2")
      BiocManager::install("edgeR")
      BiocManager::install("mixOmics")

      ---------------------
      Installation of R packages for Practical 3

      install.packages("pheatmap")

      if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

      BiocManager::install("clusterProfiler")
      BiocManager::install("org.Mm.eg.db")
      BiocManager::install("enrichplot")

      • Material

        Course material will be put online before the course.

      • Exam

        At the end of the course, you will have the opportunity to take an exam to test your newly acquired skills and earn 0.75 ECTS. 

        The exam will be an oral exam of approximately 15 minutes with the teachers, in the afternoon of the last day of the course. You will be asked to answer questions on various topics related to transcriptomics analysis.