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Nextflow for RNAseqcourse

  • Course summary

    A hands-on course applying Nextflow to a real-world transcriptomics use case: bulk RNAseq processing with Trim Galore, HISAT2 and FastQC.

    This course builds on the Hello Nextflow beginner training and demonstrates how to use Nextflow in the specific context of bulk RNAseq analysis. You will implement a processing pipeline that trims adapter sequences, aligns reads to a genome reference and performs quality control (QC) at several stages.

  • Additional information

    Technical requirements

    You will need a GitHub account OR a local installation of Nextflow. See Environment options for more details.

    Learning objectives
    • 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
    Audience & prerequisites
    • Audience: This course is designed for researchers in transcriptomics and related fields who want to develop or customize data analysis pipelines.
    • Skills: Some familiarity with the command line, basic scripting concepts, and common RNAseq file formats is assumed.
    • Prerequisites: Foundational Nextflow concepts and tooling covered in Hello Nextflow.

Course overview

This course is hands-on, with goal-oriented exercises structured to introduce information gradually.

You will start by running the processing tools manually in the terminal to understand the methodology, then progressively build up a Nextflow pipeline that automates and scales the analysis.

Lesson plan

We've broken this down into three parts that each focus on specific aspects of applying Nextflow to an RNAseq use case.

Course chapter Summary Estimated duration
Part 1: Method overview Understanding the RNAseq processing methodology and running the tools manually 30 mins
Part 2: Single-sample implementation Building a pipeline that trims, aligns and QCs a single sample, then scaling to handle multiple samples 60 mins
Part 3: Multi-sample paired-end implementation Extending the pipeline to handle paired-end data and aggregate QC reports across samples 45 mins

By the end of this course, you will be able to apply foundational Nextflow concepts and tooling to a typical RNAseq use case.

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