How can I customize the parameters for k-means and graph-based clustering in Cell Ranger?

Question: How can I customize the parameters for k-means and graph-based clustering in Cell Ranger, and what are the default values?

Answer: You can modify the following parameters related to k-means and graph-based clustering by passing a CSV file to cellranger reanalyze:

Parameter	Type	Default Value	Recommended Range	Description
graphclust_neighbors	int	0	10-500, depending on desired granularity	Number of nearest-neighbors to use in the graph-based clustering. Lower values result in higher-granularity clustering. The actual number of neighbors used is the maximum of this value and that determined by neighbor_a and neighor_b. Set this value to zero to use those values instead.
neighbor_a	float	-230	Determines how clustering granularity scales with cell count.	The number of nearest neighbors, k, used in the graph-based clustering is computed as follows: k = neighbor_a + neighbor_b * log10(n_cells). The actual number of neighbors used is the maximum of this value and graphclust_neighbors.
neighbor_b	float	120	Determines how clustering granularity scales with cell count.	The number of nearest neighbors, k, used in the graph-based clustering is computed as follows: k = neighbor_a + neighbor_b * log10(n_cells). The actual number of neighbors used is the maximum of this value and graphclust_neighbors.
max_clusters	int	10	10-50, depending on the number of cell populations / clusters you expect to see.	Compute K-means clustering using K values of 2 to N. Setting this too high may cause spurious clusters to be called.