microRNA Analysis Using Next-Generation Sequencing
From microRNA profiling and prediction to extensive downstream analyses

Understand small RNA sequencing analysis issues and solve them yourself.

In a nutshell

  • Learn the basics of different small non-coding RNAs and their characteristics
  • Understand the method of small RNA sequencing
  • Find differentially expressed small RNAs
  • Perform microRNA gene prediction
  • Analyze your small RNAs (microRNA target prediction, functional analysis, etc.)
  • Execute popular open-source microRNA tools (miRanallyzer, miRDeep, etc.) on a Windows machine (using a Linux VM)

21 - 23 September 2016

Berlin, Germany

The purpose of this workshop is to obtain a thorough understanding on the expression profiling of known microRNAs and the prediction of novel microRNA genes using next-generation sequencing technologies (NGS). The participants will be trained to understand both, the data analysis aspects of NGS technologies and the functional implications of small RNAs. Downstream analysis to infer the functional implication of the detected microRNAs will be discussed including target prediction/detection and functional analysis. After this workshop, the participants will be able to perform their own microRNA analysis using up-to-date methods and extract scientific valuable findings.

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.

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.

This workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics and comprises these three course modules:

  1. Practical Bioinformatics (with Linux):
    This module will introduce some basic commands and file formats required for small RNA-Seq data analysis.
  2. Introduction to small non-coding RNAs:
    This module will introduce the essential biological basics one needs to perform small RNA-Seq data analysis. It explains the maturation steps of microRNAs, its important secondary structure and its unique footprint in small RNA-Seq data. Furthermore, other small non-coding RNAs, like isomiRs, tRNAs, vault RNAs, ect. will be explained.
  3. Small RNA-Seq data analysis:
    In this module, novel microRNA genes will be predicted, differentially expressed microRNAs will be detected and extensive downstream analyses (microRNA target prediction, GO enrichment analysis, etc.) will be performed.

Detailed Course Program

Introduction to small RNA-Seq data analysis

  • Get introduced to practical bioinformatics with Linux
  • Understand to the small RNA-Seq sequencing protocol
  • Learn the biogenesis, the mechanism, and the function of microRNAs
  • Get to know other small non-coding RNAs (tRNAs, snoRNAs, vault RNAs, isomiRs, etc.)
  • Recognize the issues with microRNA databases

Small RNA-Seq data analysis

  • Start the Virtual Machine (VM) under Windows
  • Orientate yourself in the VM
  • Customize your VM
  • Set up your model species
  • Learn how to set up your non-model species
  • Perform small RNA profiling
  • Predict novel microRNA genes

Small RNA-Seq data analysis

  • Detect differentially expressed small RNAs
  • Generate study summaries
  • Predict microRNA target sites
  • Perform downstream analyses (GO enrichment analysis)
  • Bring everything together and extract scientific valuable findings


Prof. Dr. Michael Hackenberg (University Granada)
Michael is the main developer of miRanalyzer, one of the most-used microRNA gene prediction tools using small RNA-seq data.

Dr. David Langenberger (ecSeq Bioinformatics)
David 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 analyzed small RNA-Seq data of several large projects, for example the International Cancer Genome Consortium (ICGC).

Keynote Speakers

Prof. Dr. Peter F. Stadler (University of Leipizg)
Peter holds the chair of bioinformatics at the University of Leipzig. Over the past 25 years he has pioneered a new layer of gene regulation by non-coding RNAs (which were formerly considered as 'junk'). The last years he worked on detecting these 'hidden treasures' in RNA-Seq data sets. During his scientific career, he published more than 400 RNA related papers and articles and is Member of the Editorial Boards of seven scientific journals. ... read more

Dr. Jana Hertel (Helmholtz-Centre for Environmental Reseach - UFZ)
Janas worked on the automatical annotation of non-coding RNA genes and developed the tools RNAmicro and SnoReport. She has extensive experience with public databases for small RNAs (like miRBase, GENCODE, RFAM, etc.) and their pros and cons. ... read more


  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)

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

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)


Location: PC-College, Stresemannstra├če 78, 10963 Berlin, Germany
Language: English
Available seats: 20 (first-come, first-served)

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

Travel Information - Berlin

Key dates

Opening Date of Registration: 1 February 2016
Closing Date of Registration: 1 September 15 August 2016
Workshop: 21 - 23 September 2016 (8 am - 5 pm)


"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
Email: events@ecSeq.com