Data from: RPASE: individual based allele-specific expression detection without prior knowledge of haplotype phase

Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.基因表达变异被认为对表型多样性与分化具有重要贡献。等位基因特异性表达（allele-specific expression, ASE）分析可为基因表达调控研究提供关键见解。我们开发了一种名为RPASE（Read-backed Phasing-based ASE detection，基于读段定相的等位基因特异性表达检测）的新型方法，用于筛选呈现ASE的基因。该方法仅以单个个体的比对后RNA-seq数据，以及同个体的单核苷酸多态性（single nucleotide polymorphisms, SNPs）列表作为唯一输入，能够整合多个连锁SNPs的信息，并完成基于个体的基因水平ASE检测。RPASE在模拟实验与对照比较中表现优异。我们将RPASE应用于多种鸟类，发现了ASE潜在的丰富分布格局。