RNA-seq Workflow

RNA sequencing (RNA-seq) is a technique used to measure gene expression levels and identify transcript variants across the genome.

In this tutorial, we’ll run an RNA-seq pipeline using HISAT2 for alignment and featureCounts from the Subread package for quantification. The workflow is divided into two parts — this tutorial covers Part 1: HISAT2 alignment. Part 2 will cover differential expression analysis with DESeq2.

An installation script is included and can be downloaded from the Bioinformatics Hub extension. Note that HISAT2 and featureCounts each require their own conda environments. If no conda environment is provided, the nodes will default to using system environment variables.