Question: How can I regress certain genes such as cell cycle genes from my analysis?
Answer: At this time, Cell Ranger does not correct for cell-cycle effects.
It possible to do this with Seurat, but please note this is a third party tool that is not supported by 10x. Here is a Seurat tutorial for Cell Cycle Scoring and Regression: Seurat Cell Cycle Vignette.
Once you have identified the genes you want to remove from the analysis, you can use cellranger reanalyze. The --genes option in this tool can be used to reanalyze the data with only a subset of genes, or the --exclude-genes option can be used to exclude a set of genes from analysis. Please see Customized Reanalysis using cellranger reanalyze.