Detection and removal of barcode swapping in single-cell RNA-seq data

• DOI: 10.1038/s41467-018-05083-x
• Publication Date: 2018-07-04T09:40:57Z
• Authors: Jonathan A. Griff...; Arianne C. Richard; Karsten Bach; Aaron T. L. Lun; John C. Marioni
• Keywords: Barcode; Massive parallel sequencing; RNA-Seq

Abstract Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina machines. This may compromise validity numerous genomic assays; however, severity and consequences barcode remain poorly understood. We have used two statistical approaches to robustly quantify fraction swapped plate-based single-cell RNA-sequencing datasets. found that approximately 2.5% were mislabelled HiSeq 4000, which is lower than previous reports. observed no correlation concentration free across plates. Furthermore, we demonstrated generate complex but artefactual cell libraries droplet-based studies. To eliminate these artefacts, developed an algorithm exclude individual molecules 10x Genomics experiments, allowing continued use cutting-edge machines for assays.