Subsetting cells from a previously integrated Seurat dataset (scRNA-seq)

Question

[miyeok]

Hi all,

i have an issue of subclustering from the Seuat single cell clusters.

i already normalized, and integreted data when i made clusters from the cells of the samples.

and i wanted to subset a "T cell" cluster and analyze subclusters of that.

in that situation, should i have to go through findvariablefeatures(), and normalize data, integration process again?

i'm so confused, because in my opinion i have to do re-findvariablefeatures in the subsetted cluster. but at the same time i have doubts about renormalization and reintegration because i think that is too much.

Any of your answer would be appreciated.

Thank you

Answer 1

[DARLOR]

Hi, you don't need to do reintegration, just recalculate findvariablefeatures and normalization of data.

[heidenreich.ac]

Hi, thanks for the Q and the A! I wonder if it's necesary also to ScaleData after the subset process.