I have a query. I am trying to align my Plasmodium scrnaseq data against combined reference genomes of Human and PF3D7. Since these cells are from ring stage, the number of genes expressed is really low (25-50 genes expressed per cell on an average) and so are the UMIs. This matches with the Neutrophil's case study explained by 10X here. I am however, preplexed, when I force the number of cells to be 10k I get 17K cells as an output. Though after removal of human genes and cells according to following filtering criteria (
CreateSeuratObject(counts = counts(seurat_data), project = name, min.cells = 3, min.features = 10)), I get around 9K cells vs 3K gene matrix, I am worried if something wrong might be happening when the cells are estimated when aligning to multiple genomes?