I am comparing the gene expression of 2 bacteria under 1 condition. I have now the count tables for 3 tech. replicates for each bacteria.
Bacteria1_1.count Bacteria1_2.count Bacteria1_3.count
...same for the other bacteria.
These files look like this:
gene1 10000 gene2 500 gene3 0 gene4 5000
I want to use DESeq2 for differential gene expression analysis. But I cannot figure out how to properly execute the DESeqDataSetFromHTSeqCount() command with this type of data.
Is there another intermediate step to add ?