{"doi":"10.1101/2024.01.21.576391","title":"STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads","abstract":"Abstract Summary 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 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 Implementation STAR+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/ . Contact dobin@cshl.edu Supplementary information Supplementary data are available at Bioinformatics online.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484104,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9514,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":11793,"name":"Alexander Dobin","orcid":"0000-0002-4115-9128","position":1,"is_corresponding":false},{"id":1325702,"name":"Rebecca Asiimwe","orcid":"0009-0002-1285-1614","position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":null,"created_at":"2026-07-19T02:07:38.055693Z","pmid":"38370773","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}