Nature Communications (Jun 2020)

Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing

  • Rick Farouni,
  • Haig Djambazian,
  • Lorenzo E. Ferri,
  • Jiannis Ragoussis,
  • Hamed S. Najafabadi

DOI
https://doi.org/10.1038/s41467-020-16522-z
Journal volume & issue
Vol. 11, no. 1
pp. 1 – 8

Abstract

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Sample index hopping results in various artefacts in multiplexed scRNA-seq experiments. Here, the authors introduce a statistical model to estimate sample index hopping rate in droplet-based scRNA-seq data and show that artifacts can be corrected by purging phantom molecules from the data.