I performed RNAseq on samples where I infected bacteria with phage & incubated at different time points. This may not matter too much, but I am wondering if I should map the data back to the phage genome and bacterial genome separately, or just to the lysogen (complete genome available on NCBI). I am not entirely sure if my phage exhibits site-specific integration, and so I am wondering if this will alter counts later down the road.
Appreciate any advice on this,
Alexa