In my scRNA seq experiment, single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3′ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics) according to the manufacturer’s protocol. About 8700 cells were added to each channel with a targeted cell recovery estimate of 5000 cells.
However, after processing my raw data with CellRanger software, I get 737,280 cells (barcodes) and about 31,000 genes. I cannot understand why I get so many cells and why this barcode whitelist is not up to 10,000 cells. After filtering this data retaining genes expressed in >= 5 cells as well as retaining cells with at least 200 detected genes, I get around 2200 cells.