### code for Louder et al. submitted Nature Communications
main analyses shown in home directory
00 shows how fst was estimated using WGS (pipeline to generate input found under wgs/)
01 shows how reference was prepared, including masking SNPs using results from former fst analysis
02 shows how rnaseq reads were aligned and counted
03 shows how analyses of differential expression using pure, parental forms were conducted
04 shows how analyses of allele specific expression were conducted, including calling SNPs using RNAseq data and summarizing read counts by snp and gene
05 shows how analyses of transgressive expression were conducted
original RNAseq data can be found on the SRA
analyses requiring wgs (e.g., estimating ancestry for hybrids and fst between pure forms) shown in wgs/