RNA-seq Bioinformatics: A Practical Introduction
Mapping, Visualization, Basic Analyses

May 13th - 14th 2013

Leipzig, Germany

Scope and Topics

The purpose of this workshop is to get a deeper understanding in High-Throughput Sequencing (HTS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing machines and their implications on data analysis will be discovered. The participants will be trained on understanding their own HTS data, finding potential problems/errors and finally start writing their own pipelines. In the course we will use a real-life RNA-seq dataset from the current market leader Illumina.

All analyses will be performed using cloud services. By saving their final cloud-images, the participants will be able to reuse all tools/pipelines and to continue their analyses after the workshop (platform independently: Windows, Mac OS, Linux).

This course will be limited to 15 participants, ideally with similar knowledge base, to allow personal assistance and efficient learning. After registration, participants will be selected on the basis of their background and in order of incoming registrations.

By the end of this workshop the participants will:

  • be familiar with the sequencing methods from various instruments:
    • Illumina HiSeq 2000
    • Roche 454
    • Ion Torrent
  • be aware of the different error sources of these machines
  • understand common data formats and standards
  • know relevant tools for HTS data processing
  • automate tasks with shell scripting to create reusable data pipelines
  • perform basic analyses (gene quantification, differential expression)
  • plot and visualize results
  • be able to reuse all analyses via the employed cloud environment


  • 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, ...)

Target Audience

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

Included in Course

  • Course materials
  • Catering
  • Cloud computation resources
  • Conference Dinner


  1. Introduction to Sequencing Technologies (from a bioinformatics/data analyst view)
    • Mechanisms of instruments: Illumina, 454, IonTorrent
    • Sequencing Protocols (mRNA-seq, micro RNAseq, …)
    • Capabilities & Limitations: Error Sources, Biases & beyond
  2. Output File Formats (fastq)
  3. Preparation of raw reads: Quality-Control, Adapter Clipping
  4. Computation in the cloud
  5. Read Mapping
    • Alignment methods
    • Mapping tools, mapping to a reference genome
  6. Mapping Output
    • file formats (SAM/BAM)
    • samtools
    • bedtools
  7. Visualization of mapped reads
    • UCSC: data format for upload
    • IGV (local)
  8. Gene Expression Quantification
  9. Differential Expression Analysis (with DEX-seq)


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).

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

Mario Fasold (ecSeq Bioinformatics) works in the analysis of microarray data since 2007 and developed several tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he has analysed HTS datasets in several projects.

Ole Menssing (Illumina)

Key Dates

Closing Date of Applications: March 1st 2013
Confirmation of Attendance: March 4th 2013
Workshop: May 13th-14th 2013 (8:00 - 17:00)


Location: UFZ Conference Venue, Leipzig, Germany.
Language: English
Available seats: 15

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


ecSeq Bioinformatics
04275 Leipzig
Email: email image

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