This tutorial provides a step-by-step guide on how to analyze bulk RNA-Seq data. We will discuss the key steps involved in RNA-Seq analysis and demonstrate how to use the CHIRP pipeline, a state-of-the-art software workflow used at the Minnesota Supercomputing Institute. CHIRP has been featured in over 30 high-impact publications and continues to be a reliable tool for RNA-Seq analysis.

By the end of this tutorial, you will understand:

• The inputs and outputs of bulk RNA-Seq analysis
• How to use the CHIRP workflow to obtain relative expression data from FASTQ files
• How to assess library quality
• How to analyze and identify differentially expressed genes between conditions

This tutorial assumes basic familiarity with Linux commands, but additional resources are available for a more detailed introduction.

What This Tutorial Covers

• Steps involved in bulk RNA-Seq analysis
• Using the CHIRP workflow for data processing
• Generating a counts matrix for downstream analysis
• Performing differential expression analysis