RT Journal Article
SR Electronic
T1 Detection and removal of barcode swapping in single-cell RNA-seq data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 177048
DO 10.1101/177048
A1 Jonathan A. Griffiths
A1 Aaron T.L. Lun
A1 Arianne C. Richard
A1 Karsten Bach
A1 John C Marioni
YR 2017
UL http://biorxiv.org/content/early/2017/08/16/177048.abstract
AB 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.