Simulation-based benchmarking of isoform quantification in single-cell RNA-seq
Herrera, Marcela S
Ferguson-Smith, Anne C
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Westoby, J., Herrera, M. S., Ferguson-Smith, A. C., & Hemberg, M. (2018). Simulation-based benchmarking of isoform quantification in single-cell RNA-seq. [Journal Article]. https://doi.org/10.1186/s13059-018-1571-5
Abstract Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing quantification methods has not been established. We carry out a benchmark for five popular isoform quantification tools. Performance is generally good for simulated data based on SMARTer and SMART-seq2 data. The reduction in performance compared with bulk RNA-seq is small. An important biological insight comes from our analysis of real data which shows that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.
External DOI: https://doi.org/10.1186/s13059-018-1571-5
This record's DOI: https://doi.org/10.17863/CAM.32140
Rights Holder: The Author(s).