I am going to analyze a pair of bulk and single-cell RNA seq data. Although the ultimate goal will still be getting the DEGs from the datasets (side-by-side), I would also like to extract the normalized count for both datasets (for plotting bar chart/ PCA etc). I wonder are there any programs that support input of both bulk and single-cell RNAseq and can perform the normalization reliably? I acknowledge that the word reliably is vague and I tried to read some open thread and literature and found that seems EdgeR with quasi-likelihood approach (QLF) and including the cellular detection rate (the fraction of detected genes per cell) as a covariate (edgeRQLFDetRate) is a good option for me. However, I found that the paper used TPM as input in most of their analysis (please correct me if I am wrong). May I confirm that whether TPM can be used as the input for either DESeq2 or EdgeR? If not, whether the method described in that nature method paper can still be used for extracting the normalized count matrix?
I also have a similar question that more specifically asks the input format for either DESeq2 and EdgeR.
