I have performed clustering on my Seurat object and I would like to focus on one specific cluster and find study its subclusters. To do this, I understand that you have to subset the Seurat object. However, do I also have to run FindVariableFeatures() on this subset and then RunPCA again to find the appropriate dimensions to proceed with dimensionality reduction? I ran it with both this and without it and it yielded quite different results. Not sure which process is correct. Any help is appreciated.

Thank you Andrew. I appreciate the help.

Hi Andrew, Do we still have to run

`NormalizeData`

and`ScaleData`

, as well as`FindVariableFeatures`

and`RunPCA`

?You shouldn't have to run

`NormalizeData`

again since it's just doing a log transformation and multiplying by a scaling factor, but the others, yes.Thank you!