Index

1. OS and software prerequisites
2. Git and Github
3. Docker
4. eQTL mapping
5. Basics of Machine Learning: applications in bioinformatics
6. RNA-seq data analysis: differential gene expression
Contact

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. 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.

5. Basics of Machine Learning: Applications in Bioinformatics

Machine learning, or the study of computer algorithms that improve automatically through experience, has a number of emerging applications in the field of Bioinformatics. Here we will cover the basic aspects of supervised and unsupervised learning algorithms through a series of video lectures (slides) and hands-on sessions, focusing on actual Bioinformatic applications. A second version of the course which focuses on algorithm implementation is avaliable here.

6. RNA-seq data analysis: differential gene expression

RNA-seq enables large-scale transcriptome profiling. In our slides we will cover the basics of RNA-seq technology and data analysis. In our hands-on session (video) we will perform a differential gene expression (DGE) analysis between peripheral blood samples from subjects with influenza and bacterial pneumonia.

Contact

Diego Garrido Martín
dgarrido@ub.edu
Department of Genetics, Microbiology and Statistics
Faculty of Biology
University of Barcelona (UB)
Av. Diagonal, 643 - 08028 BARCELONA (SPAIN)

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