I need to compare some samples from different bulk RNA-Seq with some clusters of a scRNA-Seq (not whole sample) to find DEGs. We have undifferentiated samples performed by bulk RNA-Seq and fully differentiated samples (mature ones) are 2-3 clusters of a scRNA-Seq project. What I suppose to do is the do batch correction between them and find the DEGs.
However, I am not sure how precise would be such analysis? because they have completely different samples and have different amount of read counts. I got the raw counts and also cluster's raw read count from Seurat object.
How can I perform such analysis ? I think this would have some big problems, different in number of samples in scRNA-Seq and Bulk RNA-Seq, read count amount.