Bulk RNASeq analysis for differential expression

Bulk RNASeq analysis for differential expression

advanced bioinformatics


Start date:

09 September 2019


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

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



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


Differential expression analysis in R
Characterization of DE genes

Practical info

Location & Venue
Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven

Public transport
Park Inn by Radisson Leuven
Public transport

The hotel is located 300m from Leuven Central Station. The hotel connects to Leuven Central Station by a pedestrian bridge.

Route description
Park Inn by Radisson Leuven

Park Inn hotel has no own parking. It is possible to park underground in P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven.

Venue contact
Park Inn by Radisson Leuven
Location contact

+32 16 61 66 02