21-25 October 2019
This course will introduce researchers and technical workers to the bioinformatic analysis of large epigenomic data sets obtained using Next-Generation Sequencing (NGS) technologies, with a focus on ChIP-seq, RNA-seq and DNase-seq / ATAC-seq. The course will cover the theoretical foundations of the most widely adopted algorithms and analysis pipelines, a targeted introduction to scripting in bash and R/BioConductor, and extensive hands-on tutorials using publicly available NGS data sets. At the end of this course, the students should be able to efficiently analyze their own data and identify common pitfalls of genomics data analyses.
The course is aimed at researchers moving the first steps in epigenomic data analysis and / or interested in learning more about this subject. The course will offer a balanced mixture of lectures and hands-on practical tutorials using popular tools and R/BioConductor packages. Previous knowledge of genomics data formats from Illumina sequencers and exposure to bioinformatics is beneficial but not a necessary prerequisite.
Monday – Classes from 09:30 to 17:30 - “The basics”
Session 1: Motivation and introduction to the biological system_(morning)
We will start with an introductory lecture presenting several examples of integrative epigenomic data analyses from recent literature. We will then focus on the biological system that will be used throughout this 5-days course, where we will study dynamic chromatin changes induced by Lipopolysaccharide (LPS) stimulation of mouse bone marrow-derived macrophages.
Session 2: Introduction to Linux and bash (morning)
In this session, we will provide a targeted introduction to Linux and bash scripting, with a focus on the tools required for the rest of the course. No previous exposure to scripting is strictly required. Also, we will not attempt to provide a catalogue of functions and command syntax. Rather, we will focus on the principles and logic of scripting.
Session 3: R programming_(afternoon)
In the afternoon, we will cover the basics of R programming. This session will alternate short talks covering the basics with extensive hands-on tutorials to allow students without prior exposure to R to familiarize themselves with this language in the most natural way. This session aims at building a solid foundation of R programming, and will also cover good coding practices for reproducible research.
Free University of Berlin
Course material and refreshments
Course material, refreshments, lunch and accommodation
480 € (VAT included)
795 € (VAT included)
Please click HERE to get all the information about our packages.
Registration deadline: 20th September 2019.