10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger2.0, printed on 05/07/2024

Cell Calling Algorithm

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:

1. Compute the distribution of read-pairs per UMI across the entire library.
2. Take the N01 of this distribution. This is an N-statistic that is the "opposite" of, e.g., the N99. Sort the UMIs by descending read support and find the UMI above which 1% of the read pairs are assigned. This is an estimate of the maximum of the distribution.
3. The threshold for being considered well-supported is the N01 / 3.