I would like to ask if there is a standardized procedure to predict operons in bacteria from RNA-Seq data, preferably in R. I would compare two conditions with three replicates each.
Currently I am thinking of using the CONDOP package (https://cran.r-project.org/web/packages/CONDOP/CONDOP.pdf), but I would like to hear your opinions. Maybe there is an optimum strategy for this that I haven't seen.
What do you think? What would you recommend?
Thank you very much.