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")