How to run UMAP on single cell results from 2 different runs?

Question

[bioinfo]

Hello,

I am trying to compare the results from 2 different sequencing machines. We run the same samples/libraries on both machines, analyzed using cellranger count and are just trying to compare how different the results are. I would like to do a co-embedded UMAP for both datasets. Would I use seurat to merge the 2 datasets and then use the following commands to produce the UMAP?

pbmc.rna <- NormalizeData(pbmc.rna)
pbmc.rna <- FindVariableFeatures(pbmc.rna)
pbmc.rna <- ScaleData(pbmc.rna)
pbmc.rna <- RunPCA(pbmc.rna)
pbmc.rna <- RunUMAP(pbmc.rna, dims = 1:30)
DimPlot(rna, reduction = "umap")

Is there a way to do this without having to go through most of the seurat pipeline?

Thank you

[jv]

the following may be helpful: https://satijalab.org/seurat/archive/v3.1/merge_vignette.html

Answer 1

[LChart]

Yes; if you want to visualize the impact that sequencing machine has (i.e., retain all batch effects) you can use Seurat::merge to directly combine the two objects prior to any analysis. Seurat will (if I recall) add a suffix on the redundant barcodes and treat them as different cells.