Simulation based benchmarking of isoform quantification in single-cell RNA-seq [article]

Jennifer Westoby, Marcela Sjoberg, Anne Ferguson-Smith, Martin Hemberg
2018 biorxiv/medrxiv   pre-print
Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. We carried out a benchmark for five popular isoform quantification tools. Performance was generally good when run on simulated data based on SMARTer and SMART-seq2 data, but was poor for simulated Drop-seq data. Importantly, the reduction in performance for single-cell RNA-seq compared with bulk RNA-seq was small. An important biological insight
more » ... from our analysis of real data which showed that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.
doi:10.1101/248716 fatcat:ph7jb4kvmjbkbkfsqnfmwibylu