Context & citation:
This repository contains scripts for the analysis of putative life-history genes in the brown trout Salmo trutta.
The manuscript detailing the results of this analysis is:

Link to publication here

Robert Wynne, Louise C. Archer, Stephen A. Hutton, Luke Harman, Patrick Gargan, Peter A. Moran, Eileen Dillane, Jamie Coughlan, Thomas F. Cross, Philip McGinnity, Thomas J. Colgan and Thomas E. Reed

For the present analysis, the following steps were taken:

Quality of raw Illumina reads was assessed using FastQC.

Transcript quantification was performed using Salmon.

Gene-level counts were calculated using tximport.
Differential expression analysis was performed using DESeq2.

For differentially expressed genes identified between and across treatments, Gene Ontology enrichment analysis was performed using topGO.
GO term database was constructed using datasets available from Ensembl.

Plots, such as barcharts and heatmaps, were generated using ggpubr and ggplot2.

Computational support was kindly provided by the Irish Centre for High-End Computing (ICHEC).

Some scripts contained in this repository are modifications of scripts used by Colgan et el. (2019, Molecular Ecology). If reusing scripts within the present repository, please cite the original source as well and follow instructions on reuse. The original scripts are publically available at: https://github.com/wurmlab/Bter_neonicotinoid_exposure_experiment