Abstract
We have confirmed the existence of barcode swapping in scRNA-seq data from a HiSeq 4000 machine. We have estimated the rate of swapping between libraries at 1-3%, which is lower than previously reported [2]. Swapping also occurs on the HiSeq 2500 at approximately 1/10th of the rate as on the HiSeq 4000. The effects of swapping on droplet-based data may be easily removed, though there is no obvious solution for plate-based methods. Whether or not barcode swapping will compromise downstream biological conclusions remains to be explored; clearly, however, caution will be required when analysing swapping-affected single cell RNA-seq data.
Footnotes
↵* marioni{at}ebi.ac.uk
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