AltHapAlignR

AltHapAlignR estimates transcript abundance from RNA-seq data by aligning reads to multiple alternate reference haplotypes to improve allele-specific expression quantification in polymorphic genomic regions.

Key Features:

• Alternate Reference Haplotype Integration: Incorporates multiple alternate reference haplotypes alongside the standard reference genome to improve RNA-seq read mapping accuracy.
• Gene- and Haplotype-Level Quantification: Produces transcript abundance estimates at both gene and haplotype levels, enabling allele-specific expression analysis.
• Improved Analysis of Polymorphic Regions: Enhances transcript abundance estimation in highly polymorphic regions such as the major histocompatibility complex (MHC).
• Allelic Ratio Quantification: Accurately quantifies allelic expression ratios for major histocompatibility complex haplotypes.
• Human Leukocyte Antigen Expression Analysis: Corrects underestimation of expression levels for classical human leukocyte antigen (HLA) genes observed with single-reference mapping approaches.

Scientific Applications:

• Allele-Specific Expression Analysis: Quantifies allele- and haplotype-specific transcript expression from RNA-seq datasets.
• Immunogenetics Research: Investigates expression patterns of genes within the major histocompatibility complex and human leukocyte antigen loci.
• Population and Functional Genomics: Examines haplotype-specific gene expression variation across individuals.

Methodology:

AltHapAlignR aligns RNA-seq reads to both the standard reference genome and multiple alternate reference haplotypes to reduce mapping bias and generate gene-level and haplotype-level transcript abundance estimates.