Section outline

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    Transcriptomics Analysis: RNA-seq for CRCL

    20-22 June 2022

    Lyon

    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 splicing
    10:30 - 10:45 - Coffee Break
    10:45 - 12:30 - Practicals
    12:30 - 13:30 - Lunch Break
    13:30 - 15:00 - Differential Expression analysis
    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 - Downstream analysis
    12:30 - 13:30 - Lunch Break
    13:30 - 15:00 - Practicals
    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.