Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense

This repository stores Genome and Epigenome Wide Association (GWA and EWA) results from a natural collection of Thlaspi arvense lines. The collection was grown in a glasshouse and originally published here https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010452.
In this study we used unmapped sequencing reads to quantify the amount of aphids, mildew and microbes present on each T. arvense line in our greenhouse and used this as a phenotype for GWA and EWA.

All files can be opened with Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/), using the reference genome published by Nunn et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34990041/). GWA results are filtered for -log(p)>1 in order to reduce file size and make them easy to open in IGV. We run EWA only for cytosines inside pre-defined Differentially Methylated Regions, so no -log(p) filtering was necessary for these files.

All GWA and EWA analyses were run in GEMMA (https://github.com/genetics-statistics/GEMMA) with scripts available here:

https://github.com/Dario-Galanti/multipheno_GWAS/tree/main/gemmaGWAS
https://github.com/Dario-Galanti/EWAS/tree/main/gemmaEWAS