This course will provide training on two bioinformatic pipeline core assays defined by the FAANG initiative for the study of regulatory elements in fish genomes. The content will cover the use of ChIP-seq (chromatin immunoprecipitation sequencing) and ATAC-seq (assay for transposase-accessible chromatin sequencing). Participants will be introduced to key bioinformatic steps involved in data analysis and interpretation, from raw sequence data through to peak calling, interpretation of data quality, and data integration including by use of genome segmentation methods. The concept of software containers and their use for reproducible pipeline deployment will also be explored.

Please visit the AQUA-FAANG website for more information on the project.

Who is this course for?

The primary target audience is researchers working in FAANG projects, including AQUA-FAANG, GENE-SWitCH and BovReg. Familiarity with running bioinformatic analysis of sequencing data in a Unix environment is essential for those attending this training.

What will I learn?

Learning outcomes

After this course you should be able to:

• Comprehend the aims and objectives of the Aqua-FAANG project
• Generate high-quality ChIP-seq and ATAC-seq peaks using containerised pipelines
• Apply basic knowledge in the construction and use of containerised pipelines

Course content

During this course you will learn about: 

• FAANG core assays involving ChIP-seq and ATAC-seq
• Software containers and their use in running bioinformatics pipelines
• Tools for conducting ChIP-seq analysis, for instance:
  • Genrich
  • MACS
  • ChIPseeker
• Tools for conducting ATAC-Seq analysis, for instance:
  • Genrich
  • Atacv

Funding

The AQUA-FAANG project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 817923. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which maybe made of the information contained therein.

Trainers

Registration for this event is by invitation only. Members of the FAANG community and collaborating projects will be contacted directly.