Wonder if we can learn something about reference mapping here. We have scRNA-seq data form 10x platform. We want to map barcodes to mouse immune cells. When we will use two references, we got very different results regarding fractions of immune cells. Using one reference, we see more macrophages than dendritic cells; using another reference, we see more dendritic cells than dendritic cells. I am sure someone here may have similar experience? What are your opinions or solutions? Thanks.
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