Clustering analysis for scRNA-seq

Question

[MYousry]

Hello everyone,

I run STARsolo to obtain the filtered count matrix for scRNA-seq data. Currently, I am trying to perform clustering. My goal is to obtain a file (in csv, tsv, ...etc format) that has each cell barcode and its corresponding cluster/group name/number.

I have a very little background about clustering as a beginner and I am confused. Any guidance on walking me through this process to reach my goal would be highly appreciated.

Thank you so much in advance.

Cheers, Yousry

[rpolicastro]

See the OSCA, Seurat, or Scanpy vignettes.

Answer 1

[jared.andrews07]

I'd recommend doing some reading. You're getting ahead of yourself, you should learn to import your data into R/python, perform QC, normalize, etc, before attempting to cluster. I'd highly recommend you give OSCA a close read. It's easy to follow, provides good context, and has many code examples. Even if you use scanpy or Seurat instead, it'll help you recognize why certain steps are necessary.

Answer 2

[swbarnes2]

The two most common ways to analyze single cell data are either with Seurat or with bioconductor. You can google for how to use Seurat, here's a link to the bioconductor guide:https://bioconductor.org/books/release/OSCA/