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Introductory
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Video content
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Multiple choice quiz
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Approx. 1.5 hours to complete
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Completion certificate
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Innovation Scholars Pillar 2 Course Map:
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
Technology required
To participate in the course, you will need to be able to use RStudio on your computer or log into RStudio Cloud. This will enable you to complete the coding challenges and practice what you learn in the lectures. By the end of the course, you will have a better understanding of the uses of NGS technology and how to process raw data before downstream analyses.All the example data required for the analysis is available for download and has already been processed using the NF-core
RNAseq and
ATACseq pipelines.
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
