bioRxiv preprint doi: https://doi.org/10.1101/797951; this version posted October 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Obstacles to Studying Alternative Splicing Using scRNA-seq Jennifer Westoby∗1, Pavel Artemovy2, Martin Hembergz3, and Anne Ferguson-Smithx4 1Department of Genetics, University of Cambridge , Downing Street, CB2 3EH 2Department of Genetics, University of Cambridge , Downing Street, CB2 3EH 3Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA 4Department of Genetics, University of Cambridge, Downing Street, CB2 3EH October 8, 2019 ∗Electronic address:
[email protected]; Corresponding author yElectronic address:
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[email protected]; 1 bioRxiv preprint doi: https://doi.org/10.1101/797951; this version posted October 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Abstract 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. How- ever, these studies generally did not consider the impact of dropouts or isoform quantification errors, potentially confounding the results of these analyses.