How to run UMAP on single cell results from 2 different runs?
0
0
Entering edit mode
8 weeks ago
bioinfo ▴ 20

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

single-cell seurat cellranger • 285 views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 2811 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6