I am wondering whether there are best-practices to use edgeR on single-cell (10X) data that were quantified with the Alevin module from Salmon, given that we want to use the inferential replicates that it produces via bootstrapping. I know there exists the
catchSalmon function to calculate a per-transcript overdispersion value. Alevin first of all outputs gene level counts, and second I personally prefer to perform single-cell DE between clusters on the pseudobulk level (given one has biological replicates of course).
Therefore, are there best-practices to import the inferential replicates from Alevin into edgeR and can we "sum" this inferential replicate information per single cell to the pseudobulk level?