Is OpDetect strand-specific? #3
Description
I did not find much information regarding strand specificity. While this is an interesting tool, it's also merely a loose collection of scripts which makes it difficult to track which inputs are used how and where. For example, looking the scripts shows me that strand identity is sometimes respected (integrate.py) but sometimes not (get_operons.py).
In the final result it doesn't seem to make any sensible difference between plus and minus oriented CDSs. In other words, I have the feeling that stretches of plus-oriented CDSs are acceptibly called as operons, while minus-stranded CDSs are not well captured.
The tools does not seem to have mature handling of strands, so I'm trying now to run it for each strand separately.