Nextflow for RNAseq

This training course is intended for researchers in transcriptomics and related fields who are interested in developing or customizing data analysis pipelines. It builds on the Hello Nextflow beginner training and demonstrates how to use Nextflow in the specific context of bulk RNAseq analysis.

Specifically, this course demonstrates how to implement a simple bulk RNAseq processing pipeline to trim adapter sequences, align the reads to a genome reference and performs quality control (QC) at several stages.

Let's get started! Click on the "Open in GitHub Codespaces" button below to launch the training environment (preferably in a separate tab), then read on while it loads.

Learning objectives

By working through this course, you will learn how to apply foundational Nextflow concepts and tooling to a typical RNAseq use case.

By the end of this workshop you will be able to:

• Write a linear workflow to apply basic RNAseq processing and QC methods
• Handle domain-specific files such as FASTQ and reference genome resources appropriately
• Handle single-end and paired-end sequencing data
• Leverage Nextflow's dataflow paradigm to parallelize per-sample RNAseq processing
• Aggregate QC reports across multiple steps and samples using relevant channel operators

Prerequisites

The course assumes some minimal familiarity with the following:

• Tools and file formats commonly used in this scientific domain
• Experience with the command line
• Foundational Nextflow concepts and tooling covered in the Hello Nextflow beginner training.

For technical requirements and environment setup, see the Environment Setup mini-course.