RNA-seq workshop setup on training environment

Modified

September 4, 2026

RNA-seq workshop (NZ wrasse dataset)

GitHub : https://github.com/GenomicsAotearoa/RNA-seq-data-analysis-workflow-NZ

General description: This workshop uses shell tools in the first half and R/RStudio in the second half. It uses a couple of example datasets, which needs to be pre-loaded on the REANNZ training environment in RNA_seq dir. To run this workshop in a training environment, the RStudio app can be used for the entire workshop, with the terminal functionality used for the shell commands, and then R scripts will be created and run as normal in RStudio for the second half of the workshop (which is all in R from “Exploratory analysis” onwards).

Shell modules

This workshop has been tested to work with the following modules on the REANNZ HPC:

FastQC/0.12.1
MultiQC/1.24.1-foss-2023a-Python-3.11.6
Trimmomatic/0.39-Java-1.8.0_144
STAR/2.7.10b-GCC-11.3.0-alpha

The Trimmomatic section requires the adapter files to be available too, which are currently at this path on the REANNZ HPC:

ADAPTERSDIR="/opt/nesi/CS400_centos7_bdw/Trimmomatic/0.39-Java-1.8.0_144/adapters"

Learners also will need to be able to open the HTML files generated by FastQC and MultiQC. This may require javascript to be enabled in the browser.

R Packages/libraries

This workshop has been tested to work on the REANNZ HPC using:

  • RStudio-Server Version: RStudio-Server/2024.12.1-563
  • R Version: R-bundle-Bioconductor/3.17-gimkl-2022a-R-4.3.1.

The interactive plotting library is not currently loaded in this server and failed self-install (ggiraph)

The following R packages are required:

install.packages("tidyverse")
install.packages("ggiraph")
install.packages("BiocManager")
BiocManager::install("limma")
BiocManager::install("edgeR")
BiocManager::install("DESeq2")
BiocManager::install("gplots")
BiocManager::install("goseq")

Load in the required libraries:

library(ggplot2)
library(dplyr)
library(tidyr)
library(readr)
library(forcats)
library(tibble)
library(limma)
library(edgeR)
library(ggiraph)
library(DESeq2)
library(gplots)
library(goseq)

Datasets

  • The files needed are in a directory in GitHub here: September 2026 release

  • There is also an extra copy in /nesi/project/nesi02659/Chloe_files_2026/RNAseq-nz

Contains:

├── RNAseq/
        ├──backup-files/
        ├──DataFiles/
        ├──Genome/
        ├──RawReads/