Question: Normalization before or after merging the samples in Seurat
gravatar for fouerghi20
13 days ago by
fouerghi2030 wrote:

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!

ADD COMMENTlink modified 13 days ago by jared.andrews078.4k • written 13 days ago by fouerghi2030
gravatar for jared.andrews07
13 days ago by
Memphis, TN
jared.andrews078.4k wrote:

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.

ADD COMMENTlink written 13 days ago by jared.andrews078.4k
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