Dual-RNA seq with bacteria and fungi- can you split co-culture libraries for DGE comparisons?

Hi all,

I am new to RNA seq analysis and am looking for some expertise.

I am trying to plan how to analyse dual-RNA seq data that I have been given. The data is not normal human v pathogen data but is combined fungi and bacterial samples.

We are interested in genes which are DGE in fungi in response to inhibitory bacteria and non-inhibitory bacteria. As well as DGE in inhibitory and non- inhibitory bacteria in response to being co-cultured with fungi.

The Illumina pe libraries I have (all in triplicate) are:

-Fungi only
-inhibitory bacterium only
-non inhibitory bacterium only
-co-cultured fungi and inhibitory bacterium
-co-cultured fungi and non-inhibitory bacterium only

Is it possible to split libraries from each co-culture samples into separate species and compare DEGs with the bacteria and fungi only control samples? So:

-Fungi only vs fungi from co culture with inhibitory bacteria
-inhibitory bacterium only v inhibitory bacterium only from co culture with inhibitory bacteria

And

-Fungi only vs fungi from co culture with non-inhibitory bacteria
-non-inhibitory bacterium only v non-inhibitory bacterium only from co culture with inhibitory bacteria

Or is it only possible to do dual RNAseq analysis with co-cultured fungi and inhibitory bacterium and co-cultured fungi and non-inhibitory bacterium only samples?

I’d be grateful for any advice you could give me!