News:Bioinformatics Hands-On Workshop: DNA Methylation Analysis - How to Use Bisulfite-Treated Sequencing to Find Methylated Regions
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DNA Methylation Analysis

How to Use Bisulfite-Treated Sequencing to Find Methylated Regions

When: October 20th - 21st 2014

Where: Leipzig, Germany

Scope and Topics

The purpose of this workshop is to get a deeper understanding of the use of bisulfite-treated DNA in order to analyze the epigenetic layer of DNA methylation. Advantages and disadvantages of the so-called 'bisulfite sequencing' and its implications on data analyses will be covered. The participants will be trained on understand bisulfite-treated NGS data, detect potential problems/errors and finally implement their own pipelines. After this course they will be able to analyze DNA methylation and create ready-to-publish graphics.

By the end of this workshop the participants will:

  • be familiar with the sequencing method of Illumina
  • understand how bisulfite sequencing works
  • be aware of the mapping problem of bisulfite-treated data
  • understand how bisulfite-treated reads are mapped to a reference genome
  • be familiar with common data formats and standards
  • know relevant tools for data processing
  • automate tasks with shell scripting to create reusable data pipelines
  • perform basic analyses (call methylated regions, perform basic downstream analyses)
  • plot and visualize results (ready-to-publish)
  • be able to reuse all analyses


  • basic linux knowledge (shell usage, common commands). You should be familiar with the commands covered in the Learning the Shell Tutorial
  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • basic knowledge in High-Throughput Sequencing analysis (SAM format, samtools, ...)

Target Audience

  • biologists or data analysts with no or little experience in analyzing HTS data

Included in Course

  • Course materials
  • Catering
  • Conference Dinner


  1. Introduction to Sequencing Technology (Illumina)
  2. Introduction to Bisulfite Sequencing
  3. Read Mapping (special alignment method for bisulfite-treated reads)
  4. Quality Control
  5. Data Formats (e.g. vcf, bed, bedgraph, bigwig)
  6. Overview Statistics
  7. Tools and Databases (e.g. UCSCtools, BEDtools, UCSC GenomeBrowser)
  8. Visualizing the DNA methylation genome-wide (e.g. Circos Plot, R) or in specific regions/genes (e.g. UCSC, IGV)
  9. From positions to regions: advantages and disadvantages of segmentation, windowing, and smoothing
  10. Identification of Differentially Methylated Regions (DMRs)
  11. Non-CpG Analysis (Find methylated non-CpGs)


We are very excited to announce that the participants of this workshop will work with the newly developed 'Bisulfite Analysis Toolkit' (BAT). This open-source toolkit was developed at the University of Leipzig and provides very powerful tools for the analysis and visualization of bisulfite-treated DNA-Seq experiments. Every participant will get a free copy of the toolkit together with the course materials.


Helene Kretzmer (University of Leipzig) started working on NGS data in 2011. At an early stage she specialized in DNA methylation analyses and is responsible for these within the MMML-Seq study of the International Cancer Genome Consortium (ICGC).

Christian Otto (University of Leipzig) is one of the developers of the bisulfite-treated read mapping tool segemehl and is an expert on implementing efficient algorithms for HTS data analyses.

David Langenberger (ecSeq Bioinformatics) started working with small non-coding RNAs in 2006. Since 2009 he specialized on NGS technolgies. He has been part of several large NGS projects, for example the International Cancer Genome Consortium (ICGC).

Key Dates

  • Opening Date of Registration: April 1st 2014
  • Closing Date of Registration: August 1st 2014
  • Workshop: October 20th-21st 2014 (8:00 - 17:00)


  • Location: Leipzig, Germany.
  • Language: English
  • **Available seats: 20 (first-come, first-served)

Registration fees:

  • industry rate: 850 EUR
  • academic rate: 600 EUR

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

Note: Combine this workshop with our other workshops and get 10% discount.


ecSeq Bioinformatics
04275 Leipzig


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

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