Hi. I have RNA seq data of fungal cultures with the goal of comparing gene expression of treated and untreated samples (n=3 each treatment). Upon analysis, it became clear that the initial culture used is cross contaminated (or not purified) and that I am dealing with at least 2 species in my samples/dataset. Any suggestions on how I can move forward with this? Also is there is a way to determine the "percent abundance" of each organism in each treatment? This seems similar to a metagenomics approach and Im only new in RNA seq analysis and I have no experience in metagenomics. Feel free to ask for clarifications. Thank you for your feedback!
Unless you have a "pure" refrence sample this is not feasible (you can combine two expression profiles in almost infinite ways to get the combined expression profile). If you have pure reference samples that there are many tools available - originally developed for deconvoluting samples consisting of multiple cell types.