I have a small rna dataset of 12 samples containing two replicates for specific conditions. For example,
CON1 ---> 30 million reads CON2 ---> 18 million reads T1 ---> 17million reads T2 --->15million reads E1 --->16 million reads E2 --->15 million reads F1 ---> 12 million reads F2 --->6 million reads A1 ---> 17 million reads A2 ---> 13 million reads
Using the raw counts from these conditions reports only two DEG genes, which I guess because of the huge difference in coverage between replicates. Is there any possible way to use this data to screen significant genes. Any help, suggestions or ideas in this regard would be appreciated.