RNA-Seq analysis for differential expression in GenePattern

Trainer Janick Mathys and Guy Bottu
BITS Courses TRAINING AT VIB

Goal

You will execute a complete analysis workflow to detect differential expression between two conditions by using GenePattern.

Summary

We'll go through the different steps of the workflow:

  • Quality control of the sequence reads to detect biases or contaminating adapters
  • Mapping of the reads to the reference genome with use of a transcript database model
  • Quality control of the mapping results
  • Adjusting the mapping data to compensate for artefacts like duplicates
  • Calculate transcript counts usable for differential expression and merging of count tables
  • Computing differential expression using DESeq2

Prerequisites

Familiarity with

  • the Illumina sequencing process
  • 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.

Schedule

See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

Links

Scientific topics RNA-Seq, Differential expression analysis, Gene expression
Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians