STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data

Kaminow, Benjamin, Yunusov, Dinar, Dobin, Alexander (2021) STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. (Submitted)

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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.

Item Type:	Paper
Subjects:	Investigative techniques and equipment Investigative techniques and equipment > assays Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:	Yunusov, Dinar Dobin, Alexander Kaminow, Benjamin
Communities:	CSHL labs > Dobin Lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	2021
Date Deposited:	03 Oct 2023 19:58
Last Modified:	25 Jan 2024 14:20
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41113

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