Understand small RNA sequencing analysis issues and solve them yourself.

• 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)

When? 21 - 23 September 2016
Where? Berlin, Germany
Registration: ecSeq website

Scope & Topic

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.

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.

Detailed Course Program

Day 1: 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

Day 2: 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

Day 3: 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