This repository contains scripts for the Rumex eQTL mapping project, the manuscript is in preparation.
Here's a brief description of the folders containing scripts for different analyses:
BAM_processing: RNA and WGS raw reads alignment, BAM preprocessing.variant_calling: variant calling and SNP filtering.expression: counting RNA reads from BAMs, differential gene expression analyses, and preparing phenotype files for eQTL mapping.plink: assessing LD decay, PCA, and performing Tracy-Widom test.tensorqtl: running TensorQTL for cis-eQTL mapping.eqtl: identifying eQTLs, analyzing allele frequencies, effect sizes etc.popgen: generating neutral diversity statistics