Cell type identification in scRNAseq

Question

[aimanbarki]

Hello all, I am working with the healthy data set [PRJNA562645]. I have used cell ranger pipeline to create count file and created seurat object and added the metadata info. but, I am really confuse about how to identify cell type. Can some one guide me the best and easy way for celltype identification or provide me good material to read on cell type identification method.

Answer 1

[jared.andrews07]

OSCA has a good chapter on this. There are a lot of tools at this point, but that chapter gives a decent overview of the most common methods utilized by them.

You may find SingleR a decent method to get rough annotations down. It's difficult to avoid manual annotation all together though unless you have a really solid reference in hand with the granularity in labels that you need.