Mangiamele Lab RNA-seq Resource
RNA-seq analysis for Staurois parvus using nf-core
1 About this resource
This website is a bioinformatics resource for Mangiamele Lab members learning to run RNA-seq analysis for the frog Staurois parvus.
The workflow uses nf-core, a community collection of standardized, reproducible bioinformatics pipelines. The examples focus on nf-core/rnaseq, but the same approach applies to other nf-core workflows.
Visit the Mangiamele Lab website for more about the lab and its research.
Maintained by Katarina Flöer.
This tutorial is written for people using Unity (the UMass/Five Colleges computing cluster). It assumes you are on a Mac or Linux machine. Windows users can follow along but some terminal steps may look slightly different.
2 What you will learn
By the end of this tutorial you will be able to:
- Connect to the Unity computing cluster and navigate it from a terminal
- Set up a scratch workspace for running large analyses
- Submit an RNA-seq pipeline job with nf-core and SLURM
- Interpret the quality-control reports that come out of the pipeline
- Understand what the output files contain and what to do with them next
3 How to use this site
Follow the pages in order using the sidebar on the left. Each page builds on the one before it.
If you already know a topic, you can skip ahead. But if something in a later section does not make sense, it is worth going back to an earlier page, most concepts build on each other.
Throughout the tutorial you will see the username kfloer_smith_edu in example code. Replace it with your own Unity username everywhere you see it. If you are not sure what your username is, run whoami after logging in to Unity.
4 Tutorial path
| Step | Page | What you will do |
|---|---|---|
| 1 | What is RNA-seq? | Learn what the pipeline does and why |
| 2 | File types and storage | Understand the files you will work with |
| 3 | Frog data availability | Find the lab’s data on Unity |
| 4 | Using the terminal | Learn the commands you will use most |
| 5 | Connecting to Unity | Log in to the cluster |
| 6 | Using Unity | Learn how Unity is organized |
| 7 | Set up your workspace | Create a scratch directory for the pipeline |
| 8 | Run the pipeline | Submit the nf-core/rnaseq job |
| 9 | Interpret results | Read the quality reports and count tables |
| 10 | Differential expression | Run the DESeq2 analysis in R |
| 11 | Troubleshooting | Fix common problems |
5 What you need before you start
- A Unity account (ask Lisa to register your email)
- A laptop with a terminal app (Terminal on Mac, Windows Terminal on Windows)
- Basic comfort reading and typing in a terminal, the Using the terminal page covers everything you need
You do not need programming experience to follow this tutorial. All commands are written out step by step.
6 Citation and credit
This tutorial uses community tools from nf-core and Nextflow.