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  Transcriptomics Analysis: RNA-seq

  08 - 10 May 2023

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  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.

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• Select topic Programme

  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
• Select topic Software installation

  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")
• Select topic Material

  Material

  Course material will be put online before the course.
  

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• Select topic Exam

  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.