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

ABSTRACT: Barcode swapping results in the mislabeling of sequencing reads between multiplexed samples on the new patterned flow cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays, especially for single-cell studies where many samples are routinely multiplexed together. The severity and consequences of barcode swapping for single-cell transcriptomic studies remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in each of two plate-based single-cell RNA sequencing datasets. We found that approximately 2.5% of reads were mislabeled between samples on the HiSeq 4000 machine, which is lower than previous reports. We observed no correlation between the swapped fraction of reads and the concentration

INSTRUMENT(S): Illumina HiSeq 2500, Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Karsten Bach 

PROVIDER: E-MTAB-6854 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress