Operon Predict on novel bacterial isolates

Question

[mdvs]

I would like to predict operons or transcription units on a newly assembled genome. Currently the strain have been assembled and annotated, RNAseq is also available as well as proteomics evidence.

What would be the best approach to infer transcription units?

The question is if potential genes are being co-expressed as a transcription unit.

Answer 1

[Kevin Blighe]

Hello and good morning, afternoon, or evening,

Rockhopper can do this for you, but starting from the raw FASTQ files: https://cs.wellesley.edu/~btjaden/Rockhopper/

Kevin