Differential expression analysis of RNA-Seq data with DESeq2

Author/Creator: Bernd Klaus
Curated By: Karin Sasaki
Language: R
Field(s): RNA-Seq data analysis, workflow
URL: http://www-huber.embl.de/users/klaus/teaching.html#differential_expression_analysis_of_rna-seq_data_with_deseq2


This document introduces a complete sample workflow for a typical RNA-Seq data analysis. Data import, preprocessing, differential expression and enrichment analysis are discussed.

It performs a re-analysis of the RNA-Seq data obtained by comparing the expression profiles of WT mice to mice harboring a deletion that is associated with a MYC enhancer which is required for proper lip/palate formation, analysed in Uslu et. al. – Long-range enhancers regulating Myc expression are required for normal facial morphogenesis, 2014.

All necessary steps are detailed, including the download of the raw data and the alignment as well as the creation of a count table.

Tutorial includes slides, pdf explanation and exercises.

Level: Intermediate, Advanced
Format: PDF
Time Required: 3-6
Prerequisites: Basic R
Access: none
Last Curated: 08/23/2016