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

Asiimwe, Rebecca, Alexander, Dobin (February 2024) STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads. bioRxiv. (Submitted)

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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 ASE estimations similar to the original WASP algorithm.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > alleles Investigative techniques and equipment > assays bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:	Dobin, Alexander Asiimwe, Rebecca
Communities:	CSHL labs > Dobin Lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	5 February 2024
Date Deposited:	26 Feb 2024 13:32
Last Modified:	26 Feb 2024 13:32
PMCID:	PMC10871176
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41443

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