RNAseq Workshop Day 1

Overview

An introduction to GEO (Gene Expression Omnibus) and Unix.

Requirements

We will be using the Unix terminal to run our analyses, so please ensure you have access to one.

• Mac OS and any Linux distribution will have a terminal pre-installed.
  • On Mac OS, search for "Terminal" in your Spotlight search.
• Windows users:
  • Option 1: Download a Unix subsystem (WSL) (recommended).
  • Option 2: Download MobaXterm.
  • Option 3: You can use the following commands:

    wsl --install -d Ubuntu
    wsl -l -v
    wsl -d Ubuntu
    exit #or Ctrl+D

Small Outline

• Setup & Troubleshooting
• Module 1 — GEO Basics
  • Accession types
  • Common files
  • FTP/HTTPS & Data Download
• Module 2 — UNIX Basics
  • File management and navigation
  • File inspection
  • Pipes and redirects
  • Text search

References

The count matrix dataset is from the study: GSE251845. The sequence data is sourced from this repository.

This workshop was created as part of the McGill Initiative in Computational Medicine.