pre-processing of scRNA-seq and bulk RNA-seq

[InesdeSantiago]

Hi
What kind of pre-processing do you do in the scRNA-seq and RNA-seq? Apart from having consistent gene_ids and no duplicated rows, do you do any normalisation? And if so, which one?

I downloaded pre-processed scRNA-seq data (TPM normalised) folowed the workflow to generate the B matrix. Seemed to work. Then I used VST transformed RNA-seq data and ran Cibersort.. but that didn't work very well.. Maybe I am doing something wrong?