claire-moultonbrown/barley-AMF-puccinia: Barley-AMF-Puccinia stats and RNA-seq analysis pipeline v1.0

Data and code for Moulton-Brown, Brzezinska, Orosa Puenta & Helgason "AMF primes immune genes against Puccinia hordei (Brown rust) in Hordeum vulgare but does not reduce pathogen burden". A preprint of the manuscript and supplementary material can be found on bioRxiv here: https://www.biorxiv.org/content/10.1101/2025.09.16.676302v1. RNAseq data can be found at https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1328502. This repository contains reproducible scripts for processing barley (Hordeum vulgare, MorexV3) RNA-seq data and performing differential expression and downstream analyses consistent with the manuscript Methods.