Protocol for haplotype-resolved genome comparison and allele-specific expression analysis across multiple tissues and individuals

Haplotype-resolved genome comparison and allele-specific expression (ASE) analysis are essential for understanding how genomic diversity drives phenotypic variation. However, performing these analyses reproducibly across multiple tissues and individuals remains challenging. Here, we present a protocol for haplotype-resolved genome comparison and ASE analysis, extended to enable ASE profiling across multiple tissues and individuals. We describe steps for identifying and comparing haplotype-divergent sequences and alleles. We then detail procedures for detecting variants from RNA sequencing (RNA-seq) data and identifying ASE genes. For complete details on the use and execution of this protocol, please refer to Liu et al. 1