Operon prediction in RNA-Seq - How?

Question

[R.Blues]

Hello everyone,

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.

Answer 1

[Asaf]

I think that you should build a transcriptome from each library and compare them. If this is your major goal, you can use sequencing methods that will sequence the 5' and 3' ends of RNAs to get better resolution like in here: http://www.ncbi.nlm.nih.gov/pubmed/27120414

[R.Blues]

Hmm.. yes, that is another possibility, but... wouldn't building this transcriptome create noise and false transcripts? What would you use to build it, Trinity?

Thank you very much, Asaf.

[Asaf]

I don't think it will add noise, unless the expression of the operon/gene is low. Since you have the reference genome you can use something like cufflinks