Background: Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did not consider the impact of dropouts or isoform quanti cation errors, potentially confounding the results of these analyses. Results: In this study, we take a simulation based approach in which we explicitly account for

more »

... s and isoform quanti cation errors. We use our simulations to ask to what extent it is possible to study alternative splicing using scRNA-seq. Additionally, we ask what limitations must be overcome to make splicing analysis feasible. We nd that the high rate of dropouts associated with scRNA-seq is a major obstacle to studying alternative splicing. In mice and other well established model organisms, the relatively low rate of isoform quanti cation errors poses a lesser obstacle to splicing analysis. We find that different models of isoform choice meaningfully change our simulation results. Conclusions: To accurately study alternative splicing with single-cell RNA-seq, a better understanding of isoform choice and the errors associated with scRNA-seq is required. An increase in the capture e ciency of scRNA-seq would also be beneficial. Until some or all of the above are achieved, we do not recommend attempting to resolve isoforms in individual cells using scRNA-seq.