Introduction to RNA-seq using high-performance computing (HPC)

Audience Computational skills required Duration
Biologists None 2- or 3-day workshop (~13 - 19.5 hours of trainer-led time)


This repository has teaching materials for a 2-day Introduction to RNA-sequencing data analysis workshop. This workshop focuses on teaching basic computational skills to enable the effective use of an high-performance computing environment to implement an RNA-seq data analysis workflow. It includes an introduction to shell (bash) and shell scripting. In addition to running the RNA-seq workflow from FASTQ files to count data, the workshop covers best practice guidlelines for RNA-seq experimental design and data organization/management.

These materials were developed for a trainer-led workshop, but are also amenable to self-guided learning.

Learning Objectives

  1. Understand the necessity for, and use of, the command line interface (bash) and HPC for analyzing high-throughput sequencing data.
  2. Understand best practices for designing an RNA-seq experiment and analysis the resulting data.


Below are links to the lessons and suggested schedules:

Installation Requirements


Mac users:

Windows users:


These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.