Question: Can you repeat cell-calling without re-running
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.
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.