scATAC-seq: attacking open chromatin in single cells – Course and Conference Office

EMBL Course

scATAC-seq: attacking open chromatin in single cells


Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course overview

ATAC-Seq stands for Assay of Transposase Accessible Chromatin and is a widespread method to profile open chromatin on a genome-scale.

The goal of this introductory course is to teach the entire workflow of a single-cell and bulk 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 single-cell and bulk 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, comparison of bulk and single-cell data, 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.


This course is aimed at molecular biologists who want to perform ATAC-Seq experiments and/or analysis in their lab. Knowledge of bulk ATACseq, next generation sequencing technology and/or basic bioinformatics skills is desirable.

What past participants say about the course

A very well tailored course with fantastic speakers who take you on an exciting journey from wet lab to data analysis!” – Mahdi, Adam Mickiewicz University, Poland

It was an intense but very informative and motivating week. Both the theoretical and practical parts were perfectly organised. Thank you for the price-worthy experience!” – Kristyna Zavacka, Masaryk University, Czech Republic


Please see EMBL’s COVID-19 safety recommendations for testing and other requirements to attend this on-site course.


Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.


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Date: 8 - 12 Apr 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


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