Normalization before or after merging the samples in Seurat

Question

[fouerghi20]

I have 4 scRNAseq samples that I create Seurat objects for. I do the QC on each of these samples and then I merge them using the merge function from Seurat. I then normalize, scale, and run PCA on the merged dataset. Then, I take the normalized count matrix from Seurat and input it into Harmony. Do I have to normalize and scale each sample individually before merging it and normalize it again? or do I normalize only after I merge the four samples together. Any guidance would be appreciated!

Answer 1

[jared.andrews07]

Example code would be helpful, but generally you merge samples before doing anything else. Doing QC prior to merging is fine, since you should be doing that on a sample by sample basis anyway.

I'd recommend taking a look at the Seurat vignette on using it with harmony.