Single cell RNA sequencing analysis using R

Question

[fe.schiavetti]

Hi!

I’m just starting to work to a bioinformatics project where I need to conduct a single cell rna sequencing analysis using R.

My professor gave me a raw count.txt file and a raw metadata.txt file.

I now need to proceed with the analysis but I’m not sure how.

He told me to start with alignment and count of the read and create the uMAP, I know I need to create the Seurat object for that, but I’m not sure how.. can you help me? I’m at extremely beginner level

[jv]

If you already have a 'raw count.txt' then the alignment has already been completed.

Answer 1

[swbarnes2]

Go through the Seurat tutorial before you touch your own data.

If you aren't already familiar with R, this is going to be a rough way to learn.

Answer 2

[jv]

Also checkout Orchestrating Single-Cell Analysis from Bioconductor: https://bioconductor.org/books/release/OSCA/