Normalization before or after cell subset?

[moramassaro]

Hi everyone. I would like to cluster a subset of cells of my sc data. Therefore I would like to know if you recommend doing the normalization before or after my cell subset. Thank you in advance

[saketkc]

For log-normalization it would result in more or less similar results either way. If you are using SCTransform, you should normalize each experiment individually.

[moramassaro]

Thank you! So, the thing is I have a dataset from ~300k cells already clustered in three mayor groups (immune cells, epithelial cells and el otro). I've already subset epithelial cells and I'm interested on 4 subgroups of them. I want to run a pseudotime on those cells since they are lineage related. Should I subset those 4 groups first and then run SCT or run SCT on the whole epithelial dataset and then subset the groups?