News: Epigenetics Workshop - DNA Methylation Data Analysis
gravatar for David Langenberger
5.6 years ago by
David Langenberger9.5k wrote:

DNA Methylation Data Analysis

How to use bisulfite-treated sequencing to study DNA methylation



Workshop Website

15 - 17 Dec 2015

iad Pc-Pool, Rosa-Luxemburg-Straße 23, 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 to understand bisulfite-treated NGS data, to detect potential problems/errors and finally to 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

Workshop Structure and Program
This workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics. The workshop comprises three course modules.

Day 1
  Introduction to NGS data analysis
8 am
12 am
  • Introduction to Illumina sequencing method from a data analysts view
  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: Idea of adapter clipping and quality trimming 
  • Mapping output (SAM/BAM format)

  Linux for bioinformatics
1 pm
  • Introduction to the command line and important commands
  • Combining commands by piping and redirection
  • Introduction to bioinformatics file formats (e.g. FASTA, BED, VCF, WIG) and databases (e.g. UCSC, ENSEMBL)
  • Use of important bioinformatics toolkits (BEDtools, UCSCtools)
  • Introduction to R

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


Target Audience

  • biologists or data analysts with no or little experience in analyzing bisulfite sequencing data


  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • the data analysis will partly take place on the linux commandline. Is is therefore beneficial to be familiar with the commandline and in particular the commands covered in the Learning the Shell Tutorial

Included in the Course

  • Course materials
  • Catering
  • Conference Dinner


  • Helene Kretzmer (University of Leipzig) is working on DNA methylation analyses using high-throughput sequencing since 2011. She is responsible for the bioinformatic analysis of MMML-Seq study of the International Cancer Genome Consortium (ICGC).
  • Dr. Christian Otto (CCR-BioIT) is one of the developers of the bisulfite read mapping tool segemehl and is an expert on implementing efficient algorithms for HTS data analyses.
  • Dr. David Langenberger (ecSeq Bioinformatics) started working with small non-coding RNAs in 2006. Since 2009 he uses HTS technolgies to investigate these short regulatory RNAs as well as other targets. He has been part of several large HTS projects, for example the International Cancer Genome Consortium (ICGC).
  • Dr. Mario Fasold (ecSeq Bioinformatics) has developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he is specialized in the field of HTS data analysis and helped analysing sequecing data of several large consortium projects.

Key Dates

Opening Date of Registration: 1 June 2015
Closing Date of Registration: 15 November 2015
Workshop: 15 - 17 December 2015 (8 am - 5 pm)


Location: iad Pc-Pool, Rosa-Luxemburg-Straße 23, Leipzig, Germany
Language: english
Available seats: 24 (first-come, first-served)

Registration fees:

998 EUR (without VAT)

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


>>> register now




About Leipzig

Leipzig is a modern city with many students, an international flair and an established cultural scene. There many parks and an exciting night life. Leipzig features one of the largest and most beautiful christmas markets in Germany which takes place during the workshop. Take a look.

Leipzig is only about one hour away from Berlin and three hours away from Prague. It can be conveniently reached by car, bus, train or plane (for example via Leipzig/Halle Airport or one of the Berlin airports). Find more information about Leipzig on its official webpage.


ADD COMMENTlink written 5.6 years ago by David Langenberger9.5k
gravatar for David Langenberger
5.3 years ago by
David Langenberger9.5k wrote:

Feel free to download the workshop flyer and put it on your institute's notice board!


ADD COMMENTlink modified 14 months ago by _r_am32k • written 5.3 years ago by David Langenberger9.5k
gravatar for David Langenberger
5.3 years ago by
David Langenberger9.5k wrote:

Our trainers for this workshop, Helene Kretzmer and Christian Otto, used their bisulfite analysis toolkit to analyze cancer data for the ICGC (International Cancer Genome Consortium) and just published the results in Nature Genetics.

We will use exactly this toolkit in our workshop and Helene and Christian will train the participants in how to use it correctly!

Check out the publication:

Kretzmer et al.: 'DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control', Nature Genetics, doi:10.1038/ng.3413

ADD COMMENTlink modified 14 months ago by _r_am32k • written 5.3 years ago by David Langenberger9.5k
gravatar for Lars
5.6 years ago by
Lars760 wrote:

Will I have to bring my own Laptop?

ADD COMMENTlink written 5.6 years ago by Lars760

Dear Lars,

we will provide the machines. Every participant will get his/her own computer. You don't have to bring your laptop!

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.6 years ago by David Langenberger9.5k
gravatar for Antonio R. Franco
5.2 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

I am coming and hoping that the workshop will not be exclusively dedicated to the analysis of the human methylation, since I am working with plants

Can you confirm ?

ADD COMMENTlink written 5.2 years ago by Antonio R. Franco4.5k

Dear Antonio,

the examples we use in the course are only from human. In three days it is not possible to cover more than one species.

Nevertheless, you can use the same tools and analysis steps for your analysis in plants. Our trainers will surely answer all your questions regarding changes (e.g. different parameters settings) that should be performed when changing from human to plants. Furthermore, the detection of methylated non-CpGs, which occurs pretty often in plants, is included in the course. Thus, I am absolutely sure that you will be able to start analyzing your plants after the workshop.

ADD REPLYlink modified 14 months ago by _r_am32k • written 5.2 years ago by David Langenberger9.5k

Sorry, I double-checked with the trainers and this year, there will be two data sets: One from honey bee and one from human cancer

ADD REPLYlink written 5.2 years ago by David Langenberger9.5k

I just love the methylation business in bees..

ADD REPLYlink written 5.2 years ago by Antonio R. Franco4.5k
gravatar for David Langenberger
5.0 years ago by
David Langenberger9.5k wrote:

Thanks again to all participants! It was great meeting you and hopefully we'll see each other again soon!

Check our upcoming events:

ADD COMMENTlink modified 13 months ago by _r_am32k • written 5.0 years ago by David Langenberger9.5k
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