SlingShot and Subsetting data

Question

[carolofharvest]

Hello ,

I want to use slingshot package for trajectory analysis but before doing that I need to subset my annotated data to remove some clusters. Should I re scale, run PCA and runUmap functions from Seurat package again ? I dont want to re cluster my data as some cells will definetely move to other clusters if I do clustering again.

[ATpoint]

dont want to re cluster my data as some cells will definetely move to other clusters if I do clustering again.

Then don't do it? Not sure what you want to hear.

[carolofharvest]

Should I use RunUMAP or RunPCA again after subsetting ? This is my question.

[jared.andrews07]

If you don't want to change embeddings, then no. If you do, then yes.

I am also not clear as to the root of your question.