Re-integrate after removing low-quality cells?

First of all, thank you for this excellent family of packages. Our lab uses many on a near-daily basis. This is less of a technical help question and more of a discussion question:

After integration with SCVI and standard clustering procedures, I almost always find 1-3 “bad” clusters of high mito, low complexity cells and remove them. My question is: is it better to completely re-integrate the subset, or just re-cluster using the same integration vectors as before? My instinct says it’s probably fine to do the latter, but the vectors that defined those original clusters are now somewhat meaningless / have little impact on remaining cells.

Any insight you may have would be greatly appreciated, thanks!

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For small, technically-driven clusters, we don’t see much of a difference in rerunning scvi. If it was something major, you might consider rerunning (and reselecting HVG).


Thank you! This has largely been my experience as well, having now tried both approaches on the same dataset