Normalization before or after merging the samples in Seurat
Entering edit mode
17 months ago
fouerghi20 ▴ 60

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!

single cell batch effect correction seurat • 3.1k views
Entering edit mode
17 months ago

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.


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