ATAC-Seq stands for Assay of Transposase Accessible Chromatin and is, despite its recent invention, already a widespread method to profile open chromatin on a genome-scale. The goal of this course is to teach the entire workflow of an ATAC-Seq experiment including library preparation, sequencing, data processing, and downstream analysis by addressing a real biological question that will be answered at the end of the course.

We will start with the experimental ATAC-Seq protocol, highlighting the critical steps, potential pitfalls, and the most up-to-date tweaks to improve the quality of the results. After sequencing the samples we will go through the basic quality control and preprocessing steps using multiple analysis tools for next generation sequencing data. Finally, we will perform different types of analysis on the processed data, including visualisation, differential peak calling, and differential transcription factor activity profiling to come to a biological conclusion. In addition we will discuss recent advancements in technology development and algorithms for analysis and give an outlook on future perspectives and applications.