NGS Epigenomics Workshop
Exploring DNA Methylation and Chromatin Landscapes with Next-Generation Sequencing Data

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Unlock new insights into DNA methylation and chromatin landscapes with the application of bioinformatic tools for analyzing next-generation sequencing data.

In a nutshell

  • Learn the essential computing skills for NGS bioinformatics
  • Understand the basis for bisulfite-seq, ChIP-seq and ATAC-seq techniques
  • Use bioinformatics tools for exploring differential changes in DNA methylation
  • Create diagnostic graphics and statistics to support your findings
  • Integrate different layers of multi-omic data to gain insights into complex epigenomic systems

When?
November 3-5, 2025

Where?
Munich, Germany

20 votes

Scope and Topics

Unlock the secrets of gene regulation with next-generation sequencing in this hands-on workshop on epigenomic data analysis. Over three immersive days, you'll learn how to analyze DNA methylation data from bisulfite sequencing, interpret chromatin accessibility and histone modification signals, and integrate these layers to reveal functional regulatory landscapes. Starting from raw sequencing reads, you'll gain practical experience in data preprocessing, quality control, and visualization using command-line and R-based tools.

Designed for early-career researchers and beginners in the field of NGS data analysis, this workshop blends essential biological context with applied bioinformatics. All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves, with little or no background in computer science. Whether you're preparing to analyze your own datasets or aiming to deepen your understanding of epigenomic regulation, this course equips you with the skills and confidence to explore the regulatory genome.

Check our new course layout.

Our Philosophy

Get trained by experts

Our trainers have a proven record of academic and/or industrial experience in NGS data analysis. Because up-to-date expert knowledge is needed to answer your questions and know what is important in the field.

Open source NGS tools

We only use open source tools that are free to use. We try to showcase and compare different tools (e.g. NGS mappers), since not every software fits with every task/question.

Learn effectively with well-curated materials

For a optimal learning experience we carefully prepare our learning materials and example data. All materials, tools and results created during the course are for take home with you.

Workshop Design

This workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics and comprises these three course modules:

  1. Applications of NGS in epigenomic data analysis:
    Gain a solid grounding in epigenomic biology and its relationship to next-generation sequencing technologies. Explore key assays such as bisulfite-seq, ChIP-seq, and ATAC-seq, and learn how they capture different layers of epigenetic regulation. You'll also get hands-on with the Linux command line, bioinformatic file formats, and quality control practices essential for working with sequencing data.
  2. Mapping of bisulfite sequencing data and processing DNA methylation calls:
    Dive into the mapping and analysis of bisulfite sequencing data, from alignment to methylation calling. You'll learn how to handle technical artifacts, perform filtering, and begin exploratory analysis using R. By the end of the day, you'll generate summary plots, PCA, clustering, and other visualizations that lay the groundwork for downstream comparisons.
  3. Differential methylation analysis and integration of multi-omics datasets:
    Apply statistical methods to detect differentially methylated regions using real-world datasets. Explore how to integrate methylation data with ChIP-seq or ATAC-seq peak data to gain richer biological insights. The day wraps up with functional annotation, genome browser visualization, and a conceptual understanding of multi-omics in epigenomic research.

Detailed Course Program


Applications of NGS in epigenomic data analysis

  • Understand the biological context for epigenomic data analysis
  • Introduction to NGS technologies from the perspective of epigenomics
  • Understand the applications of bisulfite-seq, ChIP-seq and ATAC-seq
  • Introduction to the Linux command line and navigating the file system
  • Overview of basic bioinformatic file formats (e.g. FASTA, FASTQ, BAM)
  • Quality control and processing of sample libraries for epigenomic applications

Mapping of bisulfite sequencing data and processing DNA methylation calls

  • Understand how bisulfite-treated reads are mapped to the reference genome
  • Consider how possible errors and biases in alignments impact methylation calling
  • Perform methylation calling on a single-sample dataset
  • Familiarise with data processing in R
  • Perform post-call filtering and correction of DNA methylation values
  • Generate summary statistics and plots for comparative methylation analysis
  • Create hierarchical clustering, PCA, kernel density distributions, metagene plots

Differential methylation analysis and integration of multi-omics datasets

  • Learn different techniques for inferring differential methylated regions
  • Perform differential methylation analysis on a publicly available cancer dataset
  • Learn how to integrate with peak calling data from ChIP-seq and/or ATAC-seq
  • Relate findings to specific genomic features and perform functional analysis
  • Combine different layers of epigenomic NGS data in the genome browser
  • Apply these techniques together to gain insights on complex biological systems

Trainers

Dr. Adam Nunn (ecSeq Bioinformatics GmbH)
Adam is an expert bioinformatician skilled in developing data analysis pipelines. He specializes in bisulfite sequencing, whole genome DNA-Seq, de-novo genome assemblies, bulk RNA-Seq, and single-cell RNA-Seq. Publications

Dr. David Langenberger (ecSeq Bioinformatics GmbH)
David started working with small non-coding RNAs in 2006. Since 2009 he uses NGS technologies to investigate these short regulatory RNAs as well as other targets. He has been part of several large NGS projects, for example the International Cancer Genome Consortium (ICGC). Publications

Requirements

The target audience is biologists or data analysts with no or little experience in analyzing NGS data. A fundamental understanding of molecular biology (DNA, RNA, gene expression, PCR, ...) is assumed.

A basic knowledge of Linux & Bioinformatics (commandline usage, common commands and tools) is beneficial, but not required. You could prepare yourself with the Learning the Shell Tutorial.

Included in the Course

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)
  •   Networking opportunities
  •   Certificate
  •   Downloadable environment for seamless continuation after the course

Attendence

Location: cmt GmbH, Hansastraße 32, 80686 München, Germany
Language: English
Available seats: 20 (first-come, first-served)

Registration Fee: 1089 EUR (excluding VAT)

Travel expenses and accommodation are not covered by the registration fee.

Travel Information - Munich

Key dates

Opening Date of Registration: May 1, 2025
Closing Date of Registration: October 31, 2025
Workshop: November 3-5, 2025 (9 am - 5 pm)

What our participants are saying

"ecSeq team pays a great attention to equip you to be on your own once back alone in your lab. They are recognized experts on the field and share not only their expertise but also their experience and views. Very valuable." Marc Lamarine, Quartz Bio , Switzerland

"To go from an introduction to methylation to the complete analysis of a published data set in 3 days is an ambitious target and I am delighted that is was so comprehensively achieved. The mix between theory and practical work is very balanced. I highly recommend this course for a strong foundation in the latest methylation analysis methods. The course leaders are experts and so helpful, and to take the operating system, data and commands home at the end of the conference is a huge benefit." Kieran Meade, Teagasc, Ireland

"Very good week of course, very useful for future work on DNA methylation sequencing analysis." Jonathan Landry, EMBL, Germany

See all course reviews

When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.


Any Questions? Please feel free to contact our events team.

ecSeq Bioinformatics GmbH
Sternwartenstr. 29
D-04103 Leipzig
Germany
Email: events@ecSeq.com