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

SummaryAllele-specific expression (ASE) is an important genetic phenomenon that impacts an individuals 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 reimplementation 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. Availability and ImplementationSTAR+WASP is implemented within STAR as an integrated C++ module. STAR+WASP is open-source software, freely accessible at: http://code.google.com/p/rna-star/. Contactdobin@cshl.edu Supplementary informationSupplementary data are available at Bioinformatics online.