This is mostly a conceptual question. I have the aim of testing the hypothesis that genomic windows within an organisms genome might have higher read mapping abundances than the same region for a different organism. I am wondering if edgeR, or any other differential expression software really, would be applicable for testing this hypothesis. I understand that read mapping and differential gene and transcript expression have different - and likely harder - challenges than mapping to genic regions, and this leads me to wonder if the approaches used by edgeR, such as the TMM normalization and the shrinkage of dipersion using an empirical Bayes approach, are adequate for genomic data. Thank you for your time.