First of all, I went through related questions posted earlier. Still, I couldn't figure out the exact answer to the question I am having.
My experiment is looking at the response to a virus that infects potato. I have conducted an RNAseq study to check the gene expression after 2 and 3 days post-infection . At each time point, I have 3 biological replicates (3 infected leaves harvested, same age & same type). At the end data looks like; T2day1,T2day2, T2day3, Ctrl2day1,Ctrl2day2,Ctrl2day1 etc.
I have followed HISAT2-Stringtie pipeline to obtain gene counts as given here . The question I am having is how to provide colData in order to get the differential expression levels of each combined sample (T2day vs Ctrl2day, ....) since you have mentioned not to collapse biological samples. Is it correct If I define three biological replicates into one condition (overall four sets; trt2day, ctrl2day , trt3day, ctrl3day),
I appreciate it if you can give me insight regarding this. Thanks in advance.