I am testing some different approaches to analyse differential reads counts *per positions*, between 2 conditions with 2 replicates each. I was thinking of using DESeq2, but modified in a way that the reads counts table would contain positions instead of genes.
Therefore I would end up with a count matrix having, say 1 millions rows (instead of some thousands of rows as in the counts table usually produced by htseq-count).
What would be the performances/CPU times in this case?
Any info for parallelized computation is welcome. I know there is the option to set up parallel = TRUE by setting library(BiocParallel), register(MultiCoreParam(x)).
For instance, would that be still worth it if I would, say, use x=16, or x=32 ?