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.
Yes, you will want to re-run those steps. The variable features within that cluster and between all the others are likely very different, which will have dramatic effects on the dimensionality reduction. Without doing so, I expect it'll struggle to pull out many meaningful sub-clusters.