TY - JOUR T1 - Detection and removal of barcode swapping in single-cell RNA-seq data JF - bioRxiv DO - 10.1101/177048 SP - 177048 AU - Jonathan A. Griffiths AU - Aaron T.L. Lun AU - Arianne C. Richard AU - Karsten Bach AU - John C Marioni Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/08/16/177048.abstract N2 - 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. ER -