tfcb_2020

Lecture 19: Putting it all together using snakemake

This last session will walk through a realistic example of analyzing RNA-Seq data that will use several of the tools that we learned in the previous 18 lectures. We will combine these tools using the Snakemake workflow management system.

Learning objectives

After this session, you should be able to:

• create an annotations file for an RNA-Seq experiment that reflects the experiment design.
• outline a workflow for analyzing data from a new RNA-Seq experiment.
• implement the workflow as a Snakefile using command line tools and R scripts.
• Idnetify differentially expressed genes from RNA-Seq data.

Class materials

• RNA-Seq experiment annotations
• Snakemake workflow for RNA-Seq analysis
• Script for counting RNA-Seq reads for each gene
• Rmarkdown file for identifying differentially expressed genes