DNA Methylation Data Analysis Workshop
How to use bisulfite-treated sequencing to study DNA methylation

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Advance your epigenetics research with NGS methods.

In a nutshell

  • Learn how bisulfite sequencing works
  • Understand how bisulfite-treated reads are mapped to a reference genome
  • Perform basic analyses (call methylated regions, perform basic downstream analyses)
  • Use shell scripting to create reusable data pipelines
  • Visualize results (ready-to-publish)

When?
22. - 25. November 2016

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 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

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 this three course modules:

  1. NGS Technologies:
    Different methods of NGS will be explained and compared, together with the consequences for data analysis. The most important notations and an overview over various applications will be given.
  2. Practical Bioinformatics (with Linux):
    This module will introduce the essential tools and file formats required for NGS data analysis. It helps to overcome the first hurdles when entering this (for NGS analyses) unavoidable operating system.
  3. DNA Methylation Analysis:
    Important first NGS analyses tasks will be explained and performed. This module covers essential knowledge for analysing data of bisulfite treated DNA-Seq data.

Detailed Course Program


NGS Technologies

  • Introduction to sequencing technologies 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)

Practical Bioinformatics (with Linux)

  • Introduction to the command line and important commands
  • Combining commands by piping and redirection
  • Introduction to bioinformatics file formats (e.g. FASTA, BED) and databases (e.g. UCSC)

Introduction to NGS data analysis

  • 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)

Trainers

Dr. Helene Kretzmer (University Leipzig)
Helene 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 (Semless NGS)
Christian 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. Mario Fasold (ecSeq Bioinformatics)
Mario works in the analysis of microarray data since 2007 and developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he specialized in the field of NGS data analysis and helped analysing sequecing data of several large consortium projects.

Requirements

  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)
  • For the Introduction to NGS Data Analysis and downstream courses: basic linux & bioinformatics knowledge (shell usage, common commands and tools). You should be familiar with the commands covered in the Learning the Shell Tutorial

The target audience is biologists or data analysts with no or little experience in analyzing RNA-Seq data.

Included in the Course

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)
  •   USB-Stick for taking home results and analysis

Attendence

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

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

Travel Information - Leipzig

Key dates

Opening Date of Registration: 01 February 2016
Closing Date of Registration: 01 November 2016
Workshop: 22 - 25 November 2016 (8 am - 5 pm)

Downloads

Flyer

What our participants are saying

"The course was splendid, the instructors did a great job! It generally increased my knowledge on DNA methylation analysis and also taught me some tools/commands I can apply when handling bisulphite data." Ogechukwu Brenda Agba, Leibniz Institute for Age Research, Jena, Germany

"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, The Irish Agriculture & Food Development Authority, Carlow, Irland

"Very interesting and useful workshop. Good way to get in contact with other people in the field and have nice discussions. Objectives are clear and well explained and processed." Danny Misiak, Martin-Luther-University Halle-Wittenberg, Germany


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

ecSeq GmbH
Brandvorwerkstr. 43
04275 Leipzig
Germany
Email: events@ecSeq.com