A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples. Using simulated, merged, and pooled multi-individual datasets, we show that scSplit prediction is highly concordant with demuxlet predictions and is highly consistent with the known truth in cell-hashing dataset. scSplit is ideally suited to samples without external genotype information and is available at: Https://github.com/jon-xu/scSplit
CITATION STYLE
Xu, J., Falconer, C., Nguyen, Q., Crawford, J., McKinnon, B. D., Mortlock, S., … Coin, L. J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20(1). https://doi.org/10.1186/s13059-019-1852-7
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