Course Description

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also explore some specificities of single-cell RNAseq data analysis. Towards the end, we will cover some of the initial steps of secondary analysis, such as functional enrichment of the obtained gene lists. Participants will first start learning the concepts using small example datasets, and then will apply the learned concepts in the training room using real sized examples. At the end of the course, participants should be able to autonomously apply most of the learned methods to their own data.

Target Audience

Life Scientists who want to be able to use NGS data (RNAseq) to infer genes differentially expressed between different conditions. Computational researchers that wish to get acquainted with the concepts and methodologies used in RNAseq are also welcome.

Course Documentation

Note - All the datasets used for this training course is available in the following button. You need to unzip this file and follow the instructions throughout the documentation.

Download ADER18S Datasets File Size: 482,6MB

Day 1

1 - Plan your experiment using NGS technologies:

2 - List steps in the analysis of RNAseq differential expression experiments

    What are the steps in RNAseq data analysis

3 - Assess the general quality of the raw data from the sequencing facility

4 - Do simple processing operations in the raw data to improve its quality

5 - Generate alignments of processed reads against a reference genome

Day 2

6 - Assess the general quality of the alignments and detect possible problems

7 - Generate tables of counts

Day 3

8 - Generate lists of differentially expressed genes, at least for a simple pairwise comparison

Day 4

9 - Understand specificies of differential gene expression in single-cell RNAseq

Day 5

10 - Perform simple functional enrichment analysis and understand the concepts involved (Slides (pdf))

Learning Objectives and Course Pre-requisites


The source for this course webpage is on github.

Creative Commons License
ADER18S by GTPB is licensed under a Creative Commons Attribution 4.0 International License.