Question: Can you repeat cell-calling without re-running cellranger count?
Answer: Yes. Analysis via cellranger reanalyze will re-run cell-calling using the --force-cells parameter. You can set --force-cells to the desired cell count. If you are specifying a larger number of cells than were originally called, --matrix must specify the raw gene-barcode matrix H5 file; if you are calling a smaller number, use the filtered gene-barcode matrix H5.
The secondary analysis steps will be re-run using the updated set of filtered barcodes.
Example:
cellranger reanalyze --id=my_reanalysis --force-cells=1000 \
--matrix=my_pipestance/outs/raw_gene_bc_matrices_h5.h5
You can learn more about the --force-cells option from the cellranger reanalyze documentation.