BYASE

BYASE detects allele-specific expression at gene and isoform levels in polyploid organisms using Bayesian inference applied to single-end or paired-end RNA-seq data.

Key Features:

• Bayesian Inference Framework: Uses a Bayesian statistical model to estimate allele-specific expression at both gene and isoform levels.
• Polyploid Genome Support: Analyzes allele-specific expression in organisms with diploid or higher ploidy levels.
• RNA-Seq Data Compatibility: Processes both single-end and paired-end RNA-seq sequencing data for ASE detection.
• SNP Integration: Incorporates both phased and non-phased single nucleotide polymorphisms (SNPs) for allele assignment.

Scientific Applications:

• Allele-Specific Expression Analysis: Identifies differential expression between alleles at gene and transcript isoform levels.
• Polyploid Genomics Studies: Investigates allele-specific regulatory mechanisms in polyploid organisms.
• Transcript Isoform Regulation Analysis: Examines allele-dependent expression patterns across transcript isoforms using RNA-seq data.

Methodology:

BYASE integrates RNA-seq read data with phased or non-phased SNP information and applies Bayesian inference to estimate allele-specific expression at gene and isoform levels.