About the course

This is the documentation for the tutorial that will take place on the framework of the 'BOVREG - ATAC-Seq Workshop' course organized by the BovReg project in the Université de Limoges.

Main instructors:

Björn Langer

Gabriel Costa

Jose Espinosa-Carrasco

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Outline

This bioinformatics part of the workshop will train participants to use nf-core pipelines. nf-core is a community that maintains a set of Nextflow high-standards pipelines that perform the most common bioinformatics analyses. In particular, the practical will consist on a broad introduction on how to run nf-core pipelines with the help of the nf-core tools and a more specific section dedicated to the analysis of ATAC-seq data using the nf-core/atacseq pipeline. This pipeline was updated in the framework of BovReg to analyse the ATAC-seq data produced by the project.

Learning objectives

  • Get familiar with the nf-core pipeline repository.

  • Learn main nf-core commands for users.

  • Execute nf-core pipelines using nf-core tools.

  • Get familiar with the nf-core/atacseq pipeline and its parametrization.

  • Discuss pipeline results.

  • Run a nf-core pipeline using Tower GUI (Depending on the workshop pace).

Workshop prerequisites

  • UNIX-based environments (i.e. basic UNIX commands).

  • Being comfortable working with the CLI (command-line interface) in a Linux-based environment.

  • Familiar with scripting languages.

  • Basic knowledge of bioinformatics tools.

Being comfortable working with the CLI (command-line interface) in a Linux-based environment. .. Knowledge of containers is not mandatory. The course materials is online in the dedicated GitHub page for self-learning.

Dates, location and agenda

  • Dates: Wednesday November 9 - Thursday November 10, 2022.

  • Location: Faculty of Science and Technology - 123 Avenue Albert Thomas - Building M; Université de Limoges

Suggested agenda

Wednesday November 9

  • 09:00 - 10:30 Setup of the environment and nf-core introduction

  • 10:30 - 10:45 Coffee break

  • 10:45 - 12:00 nf-core introduction

Thursday November 10

  • 09:00 - 10:30 Introduction to the nf-core/atacseq pipeline

  • 10:30 - 10:45 Coffee break

  • 10:45 - 12:00 nf-core/atacseq results discussion