Supporting scripts for this manuscript:

Morgan AP, et al. (2019) Instability of the pseudoautosomal boundary in house mice. bioRxiv doi:10.1101/561951.

Files are organized into one directory for each of the main arms of the analysis.

• ./data: raw genotype data for intercross progeny; a kinder version is provided on Figshare
• ./genetic_map: inference of crossovers (and from that, a genetic map) in and near the PAR from genotype data in intercross progeny
• ./chipseq: re-analysis of published ChIP-seq experiments in which we used sequence variants to assign read (pairs) to parental haplotypes

Code provided here is not "one-click" reproducible -- the ChIP-seq analyses in particular require BAM files from those experiments and a large VCF file from the Sanger Mouse Genomes Project. However, the material in this repository should be sufficient for interested readers to evaluate the analyses performed and judge their quality.