Bulk RNASeq analysis for differential expression

Bulk RNASeq analysis for differential expression

Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven
Belgium

General context

  • We perform quality control of the sequence reads to detect biases or contamination
  • We map the reads to the reference genome using a transcriptome model.
  • We perform a detailed QC analysis of the mapping results to detect potential problems.
  • The mapping results are used to obtain transcript counts .
  • The count files are used to identify differentially expressed genes
  • We START a typical functional analysis of the obtained results in order to exemplify handy tools and commercial alternatives
Objectives

During this training you will:

  • execute a complete workflow at command line or in GenePattern to go from raw fastq files to count files
  • execute a complete workflow in R to detect differential expression between two conditions
  • initiate functional annotation and interpretation of the list of differentially expressed genes

 

Required skills

Familiarity with the Illumina sequencing process and with basic NGS data formats: FASTQ, SAM/BAM, GTF, ...If you do not meet these requirements you have to follow the "Introduction to the analysis of NGS data" training first.

Additionally you need to have experience in basic R programming. If you never worked in R you should attend the Basic statistics in R ​training first.

Not in the scope
  • RNA-seq assembly
  • RNA-seq analysis for isoform detection
  • RNA-seq analysis for detection of short RNA species
Course materials
Software demonstrated
  • fastQC 
  • trimmomatic
  • Groomer 
  • STAR
  • samtools
  • Picard 
  • RSeQC
  • HTSeq
  • R - RStudio - Bioconductor - DESeq2 + other packages
  • BioMart
  • ToppGene, EnrichR, iRegulon

Program

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Complete workflow from raw fastq files to count files in GenePattern or command line.
Automation of the workflow by creating a pipeline in GenePattern or running a bash script on command line

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Differential expression analysis in R
Characterization of DE genes

Practical info

Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven
Belgium

Public transport

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be