Impact of reference genome, alignment strategy, and quantification method on locus-specific HERV detection during monocyte-to-macrophage differentiation

HERVs comprise ~8% of the human genome but lack standardized locus-specific profiling workflows. THP-1 (and U937 validation) RNA-seq was aligned to GRCh38 and CHM13 with HISAT2/STAR and quantified with TE-locator/MAJEC. Mapping rates were similar (~89–93%), but quantification and DE results varied substantially by pipeline; CHM13 identified more DE HERV loci. A DE HERV near the IFNB1 promoter suggests a regulatory link to interferon signalling during macrophage differentiation.