for the initial analysis of our data set we would like to convert our single-cell RNA-Seq into Bulk RNA-Seq by summarizing the #reads per gene per sample.
I was wondering if anyone has already some experience with this kind of analysis.
Would it make sense to calculate the average expression for each gene in each sample (by dividing it with the number of cells in the sample) or just taking the
sum() of all the cells in each sample
With the count matrix created with this methodology we would like to apply standard RNA-Seq analyses such as
(for differential expression) or
Mfuzz (for time-series analysis).