Cell Ranger2.0, printed on 11/05/2024
Even though we see many putative cell barcodes in the data, only a fraction of them correspond to droplets that truly contained a cell. The remaining droplets generate background reads. The goal of this algorithm is to select the barcodes corresponding to droplets that contained cells.
First, all barcodes are assembled regardless of whether they are cell-associated or background barcodes. The algorithm requires that a cell contain at least one assembled contig with two well-supported UMIs. We require two UMIs because noise processes can generate spurious contigs that are supported by only a single UMI. The determination of a UMI as well-supported is as follows: