We got a bunch of scRNA-seq data and I've done a few tests on them. Now my boss wants me to treat them as bulk RNA-seq data and and compare the differences between treatments. Just as a test. I have not worked with bulk RNA-seq before, so I'm wondering: do you have any opinions on what I should do with these data sets? I have the digital gene expression matricies like this:
Cell1 Cell2 Cell3 -> Sample 1 Gene 1 1 2 0 3 Gene 2 0 4 0 1.33 Gene 3 0 0 1 0.33
My plan is just to add all the cells for one gene and divide all genes with the number of cells, like I show in Sample 1. Should I do some normalization first, scaling, something else? Are there any reasons why this would not be doable?