A Beginner's Guide to RNA-Seq Data Analysis Course
Quality Control, Read Mapping, Visualization and Downstream Analyses

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Advance your research. Understand NGS analysis issues and solve them yourself.

In a nutshell

  • Learn the essential computing skills for NGS bioinformatics
  • Understand NGS analysis algorithms (e.g. read alignment) and data formats
  • Use bioinformatics tools for handling RNA-Seq data
  • Compare different approaches for differential expression analysis

When?
1 - 5 February 2016

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. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. You will be trained on understanding NGS data formats and handling potential problems/errors therein.

All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this new and fast evolving research topic.

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. Linux for Bioinformatics:
    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.
  2. Introduction to NGS data analysis:
    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.
  3. RNA-seq Data Analyses: RNA-Seq for model-organisms

Detailed Course Program


Linux for Bioinformatics

  • 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)
  • Usage of important bioinformatics toolkits (BEDtools, UCSCtools)
  • Introduction to R

Introduction to NGS data analysis

  • Introduction to sequencing technologies from a data analysts view
  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
  • Introduction to read mapping (Alignment methods, Mapping heuristics)
  • Read mapping (BWA, Bowtie2, STAR, segemehl)
  • Mapping output (SAM/BAM format)
  • Usage of important NGS toolkits (samtools, BEDtools)
  • Mapping statistics
  • Visualization of mapped reads (IGV, UCSC)

RNA-seq Data Analyses

  • Understand split-read mapping
  • Run different split-read mappers (tophat, segemehl, STAR)
  • Understand the Tuxedo Suite (cufflinks, cuffcompare, cuffmerge, cuffdiff, etc.)
  • Predict new transcripts/isoforms using cufflinks/cuffmerge
  • Quantify exons/genes/transcripts
  • Predict
    • Differential exon usage using DEXseq
    • Differential gene expression using DEseq
    • Differential isoform expression using cuffdiff
  • Predict non-standard transcripts (circularized RNAs and/or fusion transcripts)

Speakers

Gero Doose (University of Leipzig)
Gero found and published several circularized RNAs in various RNA-Seq experiments. He specialized on split-read analysis some years ago and has a strong expertise in downstream analyses.

Dr. Christian Otto (CCR Bio-IT)
Christian is one of the developers of the split-read mapping tool segemehl and is an expert on implementing efficient algorithms for NGS data analyses.

Dr. David Langenberger (ecSeq Bioinformatics)
David started working with small non-coding RNAs in 2006. Since 2009 he uses NGS technolgies 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).

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: 1 Juli 2015
Closing Date of Registration: 15 January 2016
Workshop: 1 - 5 February 2016 (8 am - 5 pm)

What our participants are saying

"Good resume of the last technologies and applications. Definitly will improve the comunication with our bioinformatics colleagues for perfom the proper analysis and understanding of the data. Thanks for an intensive but nice course." Susana Gonzalez Fernandez-Nino, Bayer Crop Science, Germany

"Very valuable workshop which improved my bioinformatics understanding a lot and provided interesting aspects, I will put more focus on while analyzing our own data." Corinna Streitner, KWS Saat AG, Germany

"Excellently prepared and performed workshop. A lot of information provided." Jakub Mrazek, Czech Academy of Sciences, Czech Republic


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