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Table of Contents

1. OS and software prerequisites
2. Basics of Git and Github
3. Docker
4. eQTL mapping

1. OS and software pre-requisites

1.1. OS

Make sure your OS fulfills the following requisites:

• Linux (Ubuntu >=Trusty/14.04, 64-bit)
• Mac (OS X El Capitán >=10.11)
• Windows 7/8/10

1.2. Bash/Docker

Linux and Mac

The Bash shell is available on Linux and Mac OS. Read the documentation at Docker website to install Docker for Ubuntu or Docker for Mac.

Windows

Use VirtualBox or VMWare player to import this virtual machine with Ubuntu 18.04 and Docker pre-installed. Follow the instructions provided here.

2. Basics of Git and GitHub

Git is a version control system that enables tracking changes in computer files and coordinating the work on these files among multiple collaborators. GitHub is a web-based hosting service for version control using Git. Learn the basics about them on our slides and hands-on.

3. Basics of Docker

Docker is a software that performs operating-system-level virtualization aka containerization. This is an advanced topic and we will only cover the most basic concepts and usage. You can find here our slides and hands-on.

4. eQTL mapping

Expression quantitative trait loci (eQTLs) are genomic loci associated to the expression of one or more genes. eQTL mapping sheds light into the mechanisms underlying GWAS associations, helping to bridge the gap between the genotype and the phenotype. In our slides we will go over the main topics in eQTL mapping. In our hands-on, we will build our own eQTL mapping pipeline in the framework of the GEUVADIS project.