An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation. - Benjamin S; McElfresh GW; Kaza M; Boggy GJ; Varco-Merth B; Ojha S; Feltham S; Goodwin W; Nkoy C; Duell D; Selseth A; Bennett T; et al. (Frontiers in immunology, 2025)