16 months ago by
The main difference between scRNA-seq and standard RNA-seq is (A) a bit more complicated analysis workflow and (B) often different goals.
The additions to the normal analysis in scRNA-seq include handling cell and UMI barcodes throughout the process so you can reach a reliable matrix of values per-cell. This assumes you're using an scRNA-seq method that uses UMIs, of course. Aside from that you can mostly use the same tools.
salmon and a lot of other tools now provide options to better handle quantification of scRNA-seq data (i.e., they now make it easier), so take advantage of these options if you can.
There's often a difference in goal between the two sets of methods. Bulk RNA-seq is typically used to assess changes due to experimental conditions, whereas scRNA-seq is more frequently used to assess differences between cell types (or to find cell types). You can assess changes due to an experimental condition in scRNA-seq too, of course, though it's a bit more involved since you need to identify cell types for comparison across samples.