I have recently performed RNA-seq on two bacterial species both on their own and in co-culture. Unfortunately for me, one of the species (A) doesn't yet have a published genome that it maps nicely to... I have used rnaSPAdes to assemble a reference for A from it's monoculture growth. What I wanted to know is whether there is a way that I could filter out the reads of the other species (B) in the co-culture condition, and assemble what is left. A grows much better when co-cultured, so I want to be sure that I am not missing anything, that isn't being expressed on its own!
I hope that makes sense