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The goal of this repository is to compare the accuracy of different SNP-based demultiplexing softwares and to identify the best software(s) to use for demultiplexing PBMCs for the sceQTL-Gen Consortium.
SNP-based demultiplexing enables cells from multiple (unrelated) individuals to be mixed together before droplet-based single cell RNA-seq (scRNA-seq) experiments without the need for additional steps, reagents and costs that are required by hashing methods. The cells from multiple individuals are combined (step 1) prior to using droplet-based methods to capture thousands or tens of thousands of single cells. Then the droplets undergo library preparation and sequencing (step 2). Following sequencing, the reads undergo normal pre-processing such as the cell ranger pipeline (step 3). While reads can be mapped to cells at this stage, the individual that each cell came from is unknown. Finally, SNP-based demultiplexing methods leverage the genetic differences between each of the individuals included in the pools to identify which cells came from each individual (step 4).
