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

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.

vigalileogalilei
27/02/2022

Genome Biology

Isoform quantification

Single cell

Bulk RNA-seq

Quantifying transcript abundances

Quantification methods

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