STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads.

ABSTRACT: Allele-specific expression (ASE) is an important genetic phenomenon that impacts an individual's phenotype and is relevant in various biological and medical contexts. Next-generation RNA sequencing technologies provide an unprecedented opportunity to measure ASE genome-wide across all heterozygous alleles expressed in a given sample. One of the major obstacles to the accurate calculation of ASE from RNA-seq data is the reference mapping bias, i.e., the preferential misalignment of the reads to the reference allele. Here, we present STAR+WASP, our re-implementation of WASP, a highly accurate algorithm for reducing the reference bias (Van De Geijn et al. 2015). We show that STAR+WASP is an order of magnitude faster than WASP while significantly reducing reference bias and providing AS

SUBMITTER: Asiimwe R 

PROVIDER: S-EPMC10871176 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature