Question: When I try to run "cellranger aggr" pipeline with >128 k cells I get an error. Is there an upper limit on the number of cells that can be used with "cellranger aggr" pipeline?
Answer: Cell ranger does not have a maximum number of cells threshold when "aggr" is run without batch correction. We have validated for up to 250k cells when run on minimum compute resources. But if you have larger compute resources, you could aggr larger cell counts in Cell Ranger 3 when merging data without chemistry correction.
However, if you are using chemistry batch correction, then there indeed is a threshold of 128k cells. The chemistry batch correction is resource intensive and so considering the minimum compute resources (64 GB RAM), we have specified the 128k cell limit. If however you have sufficiently high compute resources, you can try with manually changing the limit that is hardcoded here:
CBC_MAX_NCELLS = 128000
Please note that we have not validated Cell Ranger with cell counts beyond this number and advise caution.
Also, please note that Loupe Cell Browser can load up to 1.3 million cells at this time. In addition, the differential expression analysis in Loupe Cell Browser can be done on 100k cells only.
Disclaimer: This article and code-snippet are provided for instructional purposes only. 10x Genomics does not support or guarantee modifications to Cell Ranger code base.