CompMap: an allele-specific expression read counter based on competitive mapping

Gene regulatory changes acting cis and trans to a gene can be inferred with allele-specific expression (ASE) transcriptomes from interspecies and inter-population hybrids and their parents. Problems of mapping bias and excessive information loss, however, can arise unintentionally from cumbersome analysis pipelines. We introduce CompMap, a self-contained method in Python that generates allele-specific expression counts from genotype-specific alignments. CompMap sorts and counts reads, not just SNPs, by comparing read-mapping statistics to parental alignments within homologous regions. Ambiguous alignments resolve proportionally to allele-specific counts or statistically using a binomial distribution. Simulations with CompMap show low error rates in assessing regulatory divergence.