Normalization before or after merging the samples in Seurat
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4 months ago
fouerghi20 ▴ 30

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 • 689 views
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Entering edit mode
4 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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