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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)?

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  • $\begingroup$ Care to explain downvotes? $\endgroup$ – gc5 Dec 31 '17 at 20:20
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    $\begingroup$ I haven't downvoted you but this question (to my taste) doesn't show any research effort, I think this kind of downvotes can be prevented by showing some effort to solve yourself the question, for example, showing which articles have you read about doublets (if they exists) or what kind of search have you done to find more information, even if it is unsuccessful. $\endgroup$ – llrs Feb 14 '18 at 8:08
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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 "unique" 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).

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.

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    $\begingroup$ Don't forget that doublets can also be derived from tissues that were not completely dissociated. $\endgroup$ – GWW Dec 29 '17 at 13:51
  • $\begingroup$ “less likely in cell-capture RNA sequencing” — Except that the C1 used to have a notorious flaw that messed up its doublet detection when they were z-stacked. $\endgroup$ – Konrad Rudolph Dec 29 '17 at 16:00
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"Doublet" is commonly used to describe a droplet in droplet-based sequencing that has captured atleast 2 cells. 10x states their doublet rate to be 0.9% per 1000 cells. There is a tradeoff between targeted cell capture and doublet rate and lab protocols are usually optimized for a certain expected doublet rate.

One should expect to see close to doubling of transcripts but it is not trivial to infer this computationally.

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