What are doublets in single cell RNA-seq data? I am reading The Tabula Muris Consortium et al. (pp).


  In some organs, cells with more than 2 million reads were also excluded as a conservative measure to avoid doublets.


How exactly is a “doublet” defined? For example, is doublet a set of cells sequenced as a single cell (and so, the number of transcripts is double)?
Is doublet a set of cells sequenced as a single cell?

Yes. Depending on the method of single cell sequencing it may be more or less likely for groups of cells to be captured and barcoded with the same &quot;unique&quot; barcode. This is more likely in split-pool RNA sequencing (e.g. SPLiT-seq), and less likely in cell-capture RNA sequencing (e.g. Fluidigm C1). Doublets can also be created through physical / experimental processes (e.g. from tissues that were not completely dissociated).
Bear in mind that detecting doublets is not as simple as counting for doubling of transcript expression, because the expression profiles are different in different cells. That's why single-cell sequencing is useful in the first place.