I have a data of the insect (eukaryotic) tissue transcript data that has symbiotic organism (prokaryotic) living inside this tissue. I have done RNA sequencing with the poly-A selection. so ideally there should not be any transcript from the bacteria in the dataset. But that's not the case always.
So my question is if I find any transcript that is showing strong expression in the tissue, how can I confirm that the signal is from the eukaryotic cell and not the prokaryotic cell contamination? I do not have genome data available from both organisms unfortunately.
Thank you Amol