Allim

Allim quantifies allele-specific gene expression (ASE) from RNA-seq by generating a polymorphism-aware reference genome, using sequence-specific simulations to correct mapping bias, and applying statistical tests to detect allelic imbalance.

Key Features:

• Polymorphism-Aware Reference Genome: Generates a reference genome that incorporates sequence variations between alleles to reduce mapping bias.
• Mapping Bias Reduction: Minimizes discrepancies in read alignment caused by sequence variation through the polymorphism-aware reference.
• Sequence-Specific Simulation Tool: Employs sequence-specific simulations to estimate and correct residual mapping biases.
• Statistical Testing for Allelic Imbalance: Applies statistical tests to bias-corrected RNA-seq data to identify significant allelic imbalances.

Scientific Applications:

• Genetic Research: Enables precise measurement of ASE to study how genetic variants influence gene expression and phenotypic diversity.
• Disease Studies: Identifies allelic imbalances associated with diseases to inform investigations of disease mechanisms.
• Evolutionary Biology: Analyzes allele-specific expression patterns to study evolutionary changes across species or populations.

Methodology:

Computational steps include adjusting the reference genome to reflect polymorphisms, performing sequence-specific simulation to estimate and correct residual mapping bias, and applying statistical tests to detect significant allelic imbalances in RNA-seq data.