{"doi":"10.1101/2021.05.05.442755","title":"STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data","abstract":"Abstract We present STARsolo , a comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR . Using simulated data that closely resembles realistic scRNA-seq, we demonstrate that STARsolo is highly accurate and significantly outperforms pseudoalignment-to-transcriptome tools. STARsolo can replicate the results of, but is considerably faster than CellRanger , currently the most widely used tool for pre-processing scRNA-seq data. In addition to uniquely mapped reads, STARsolo takes account of multi-gene reads, necessary to detect certain classes of biologically important genes. It has a flexible cell barcode processing scheme, compatible with many established scRNA-seq protocols, and extendable to emerging technologies. STARsolo can quantify transcriptomic features beyond gene expression, which we illustrate by analyzing cell-type-specific alternative splicing in the Tabula Muris project.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":212737,"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":471,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9416,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":307831,"name":"Dinar Yunusov","orcid":"0000-0003-3478-7203","position":1,"is_corresponding":false},{"id":11793,"name":"Alexander Dobin","orcid":"0000-0002-4115-9128","position":2,"is_corresponding":false},{"id":802959,"name":"Benjamin Kaminow","orcid":"0000-0002-2266-3353","position":0,"is_corresponding":true}],"reference_count":49,"raw_metadata":null,"created_at":"2026-07-18T23:52:27.434608Z","pmid":null,"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":[]}