ecSeq

DNA Methylation Data Analysis How to use bisulfite-treated sequencing to study DNA methylation Link: Workshop Website When? 15 - 17 December 2015 Where? 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 - 5pm 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 dataRequirements 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 Trainers 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) Attendance 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.

A Beginner's Guide to NGS Data Analysis Quality Control, Read Mapping, Visualization and Downstream Analyses When? 9. - 13. March 2015 Where? Leipzig, Germany Scope and Topics The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Additionally, all workshop participants should be enabled to perform important tasks of NGS data analysis tasks themselves. The first workshop module is an introduction to data analysis using Linux, assuring that all participants are able to follow the practical parts. The second module dicusses advantages and disadvantages of current sequencing technologies and their implications on data analysis. The most important NGS file formats (fastq, sam/bam, bigWig, etc.) are introduced and one proceeds with first hands-on analyses (QC, mapping, visualization). You will learn how to read and interprete QC plots, clip adapter sequences and/or trim bad quality read ends, get bioinformatics backgrounds about the read mapping and understand its problems (dynamic programming, alignment visualization, NGS mapping heuristics, etc.), perform your own mapping statistics and visualize your data in different ways (IGV, UCSC, etc.). The last two modules adress two specific applications of NGS: RNA-seq of model organisms and RNA-seq of non-model organisms. Workshop StructureThe 2015 workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics. The workshops comprises four course modules which can be combined. Linux for Bioinformatics: This course module is optional. It 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 analysis) unavoidable operating system. Every participant who has no background in Linux usage should attend this course! (The linux calls and commandline pipes teached here are the basis for all other courses and can not be covered again!) Introduction to NGS data analysis: This module is mandatory. Different methods of NGS will be explained, the most important notations be given and first analyses be performed. This course covers essential knowledge for analysing data of many different NGS applications. It also assures that all participants will be on the same level of knowledge for the downstream courses. RNA-seq Data Analyses: Particpants can choose up to one of the following options: RNA-Seq for model-organisms RNA-Seq for non-model organisms Depending on the organism you are working with, our trainers will show you what's possible with your data and how you could/should interprete the output data. Key DatesOpening Date of Registration: 10 November 2014 Closing Date of Early Registration: 15 January 2015 Closing Date of Registration: 1 March 2015 Workshop: 9 - 13 March 2015 (8am - 5pm) AttendanceLocation: iad Pc-Pool, Rosa-Luxemburg-Straße 23, 04103 Leipzig, Germany Language: English Available seats: 24 (first-come, first-served) Course Prices and ProgramThe prices and the program can be found on our workshop website: http://www.ecseq.com/workshops/workshop_2015-01.html ContactecSeq Bioinformatics Brandvorwerkstr.43 D-04275 Leipzig Germany Web: www.ecseq.com Email: events@ecSeq.com