Sample clustering from 10X single cell

Question

[synat.keam]

Dear Fellows and Senior,

I have single data from 10X and have done cell clustering using Seurat. I am not sure whether you guys know whether there is R tutorial or could guide me to some R script to perform sample clustering (not cell clustering) from 10X single cells sequencing? I have three distinct groups and would like to perform clustering whether they are separated from each other. Appreciate your help!

Kind Regards,

Synat

Answer 1

[jared.andrews07]

Read OSCA and/or the Single Cell Best Practices book. If you still have a question, provide an example of what you've done, the output, and what you'd like or expect instead.

In most cases, cell clustering supersedes sample clustering, as it is evident when a cluster is composed solely of a single sample, etc. Just visualizing your cells on a UMAP colored by sample will answer whether the samples are reasonably different from each other.

[synat.keam]

Thank you, professor! Appreciated you took time to respond.