Training

This course is intended to give life scientists training in the following areas: genomics, analysis of next generation sequencing data (NGS) as well as interactions and network analysis.

The first day is designed to familiarize participants with NGS data analysis and to provide hands-on computational experience in analysis of such data using common analytical approaches to RNA-Seq data handling.

The second day provides an introduction to the study of Protein-Protein Interaction (PPI) networks, their importance and the techniques that are used to build and analyze them. Data resources related to pathways will also be covered.

The third day will provide an introductory overview of the Ensembl Plants project (http://plants.ensembl.org), which provides a comprehensive and integrated source of annotation of plant genome sequences, including genes, sequence variation and comparative genomics.  Data will be explored through hands-on exercises in the use of the browser in an interactive day.

What will I learn? 

• What are the fundamental principles in the analysis of RNA-seq data. Topics will include: data quality, alignment, data handling and visualization, region identification, transcriptome analysis and basis statistical analysis.

• To understand what is to be found in a molecular interaction database, alternative data formats and the various tools designed to work with them.

• To learn how to explore reactions and pathways.

• Understand the data in Ensembl Plants, from the perspective of genome annotation

• Gain practical knowledge in how to view gene sequences, comparative genomics data (gene trees and homologies) and sequence variation using the Ensembl Plants browser (http://plants.ensembl.org).

• Complement Ensembl Plants browsing with the data mining tool BioMart.