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Innovation Scholars Pillar 2 Course Map:
Welcome to our NGS: ATAC-seq course where you will gain a comprehensive understanding of how to analyse and visualise ATAC-seq data.
! Before taking this course, it is important to understand the basics of NGS by taking the NGS: Introduction and pre-processing pipeline course.
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
- You require flexible learning format
- You need to start using ATAC-seq data
- You want to gain a better understanding of what information you can get from ATAC-seq data
- You would like to learn how to carry out differential accessibility 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.
Learning objectives
- Obtain a clear understanding of how ATAC-seq data are analysed and visualised
- Understand how peaks are called
- Perform differential accessibility test
- Use R to read NGS data and annotate features
- All the example data required for the analysis is available for download and has already been processed using the NF-core ATACseq pipelines.
