Description:

Welcome to our Next-Generation Sequencing (NGS) Introduction course where you will gain a comprehensive understanding of how NGS work, how different types of NGS can answer different biological questions and how the raw data processing is in common between the different platforms with a particular focus to bulk RNA-seq and ATAC-seq. This introduction is preparatory for our RNA-seq, ATAC-seq and variant analysis using Galaxy courses where we will go through the specific analyses after the pre-processing steps.

This course is for you if:

• You have basic knowledge of R programming language which may have been obtain via our Pillar 2: Basic R with Data Carpentry course
• You work in a biomedical field and you want to learn how to pre-process NGS data
• You require flexible learning format
• You want to gain a better understanding of what NGS is used for
• You would like to learn how to carry out differential expression (RNAseq) or differential accessibility (ATACseq) tests for bulk data

Learning objectives

• Obtain a clear understanding of how NGS data is generated and the different types of questions which can be addressed using this technology
• Understand the principles of NGS data pre-processing and genome alignment
• Perform quality control using two examples: ATAC-seq and RNA-seq
• Use R to read NGS data and annotate features