Bulk RNASeq analysis for differential expression

advanced bioinformatics
live training

Bulk RNASeq analysis for differential expression

Target Audience:
VIB PhD Student
VIB Postdoc
VIB Staff Scientist
VIB Group leader & Expert
VIB Technical support
Location:

Leuven

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
Training material
Software demonstrated
  • fastQC 
  • trimmomatic
  • Groomer 
  • STAR
  • samtools
  • Picard 
  • RSeQC
  • HTSeq
  • R - RStudio - Bioconductor - DESeq2 + other packages
  • BioMart
  • ToppGene, EnrichR, iRegulon

Program

-

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
Leuven - Park Inn by Radisson

Martelarenlaan 36
3010 Leuven
Belgium

Public transport
Leuven - Park Inn by Radisson
Public transport

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

Route description
Leuven - Park Inn by Radisson
Parking

Park Inn hotel has no own parking. It is possible to park underground in P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or in parking De Bond, Martelarenlaan 18, 3010 Leuven.

Venue contact
Leuven - Park Inn by Radisson
Location contact

+32 16 61 66 02

sales.leuven@parkinn.com