This course was designed for students who have a background in molecular biology and are interested in learning how to analyze RNA sequencing (RNA-Seq) data. RNA-Seq is an analytical method which measures the amount of RNA that has been transcribed from each gene. It involves some sophisticated molecular biology, expensive instruments, and generates large volumes of data which are beyond what standard office software and laptops can handle. This means that you will need to use both specialized software and remote high- performance computing systems. In order to work with these systems, you will need to learn some basic programming skills. This course is designed to help you learn these skills and to apply them to RNA-Seq analysis.

This course is designed for students who have some background in molecular biology and no background in programming.

You should have some background in molecular biology. Specifically, you should be able to:

• define what DNA is and understand its role in the cell,
• define what RNA is and understand its role in the cell,
• understand the cellular process of transcribing DNA into RNA and translating RNA into protiens.

After complering this course you should be able to:

1. Understand what RNA-sequencing is and what kind of data it produces.
2. Write short scripts in the bash programming language which use variables and loops.
3. Assess the quality of an RNA-Seq experiment using FastQC and MultiQC.
4. Decide whether to trim the reads and know how to do this using fastp.
5. Align reads to a reference genome using STAR and quantify gene counts using RSEM.
6. Read in, analyize, and plot data using the R programming language.
7. Identify differentially expressed genes between experimental groups from an RNA-Seq experiment.
8. Identify differentially expressed biological pathways between experimental groups from an RNA-Seq experiment.