Latest version of the eQTL Catalogue RNA-seq quantification workflow can be found here: eQTL-Catalogue/rnaseq.

Introduction

nfcore/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.

The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) and performs extensive quality-control on the results (RSeQC, dupRadar, Preseq, edgeR, MultiQC). See the output documentation for more details of the results.

Additionally, the pipeline is expanded to be able to quantify transcript, exon, alternative splicing and TxRevise expressions. See optional quantification methods for details.

The pipeline is built using Nextflow, a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nfcore/rnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Amazon Web Services (aws)
   • Swedish UPPMAX clusters
   • Swedish cs3e Hebbe cluster
   • Tübingen QBiC
   • CCGA Kiel
   • Adding your own system
3. Running the pipeline (Gene expression)
4. Running the pipeline (With additional quantification methods)
5. Output and how to interpret the results
6. Troubleshooting

General overview

The schema shown below represents the high level structure of the pipeline.

Credits

These scripts were originally written for use at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden, by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn).

Many thanks to other who have helped out along the way too, including (but not limited to): @Galithil, @pditommaso, @orzechoj, @apeltzer, @colindaven.