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!
How were these libraries prepared? Different prep methods are needed for pro- and eukaryotic libraries.
For the question above answer is yes as long as you have good reference genomes available you should be able to bin/split the reads using
bbsplit.shfrom BBMap suite.Just leaving this excellent reference by the Vogel Lab describing principles of dual RNA-seq for future readers of this post.