Kaminow, Benjamin, Yunusov, Dinar, Dobin, Alexander (2021) STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. bioRxiv. (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: | |
| Communities: | CSHL labs > Dobin Lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 2021 |
| Date Deposited: | 03 Oct 2023 19:58 |
| Last Modified: | 16 May 2024 19:33 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/41113 |
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