Hello, I have a pathosystem of host and obligate pathogen. There are three strains of host which is treated with two different strains of pathogens. I have RNA seq reads for these treatments described below and have 3 replicates for each treatment
a. Host 1 is treated with Pathogen 1 and Host 2 is also treated with pathogen 1. b. Host 1 is treated with Pathogen 2 and Host 3 is also treated with pathogen 2.
The experimental setup I have in mind is to do a pair wise comparison between the two treatments in (a) and same in (b). What I'm interested is to look for the genes that are highly up/down in pathogen strains during the infection.
We don't have a control for the pathogen as it is an obligate parasite. So , i would like to know if this comparison between treatments is sensible?
Would there be any other way to handle this condition. Any suggestions would be very helpful.