Hierarchical Analysis of Multi-mapping RNA-Seq Reads Improves the Accuracy of Allele-specific Expression

RNA-seq experiment on reciprocal F1 hybrid cross between two diverse mouse strains NOD/ShiLtJ and PWK/PhJ to study the extent of Allele-specific expression (ASE) and the cause of ASE. Overall design: Illumina 68bp single-end RNA-seq data from 48 reciprocal F1 mice. 24 male F1 progeny from each cross direction with two age and diet groups. In total, there are eight groups defined by three experimental factors cross-direction, diet and age with six biological replicates per group.