Optimizing DirecTag Params via DeNovoGUI

[Andrew Ottens]

I've been exploring DeNovoGUI and have been digging around to find further information on DirecTag, which no longer is available directly from Dr. Tabb's laboratory.  

Gone with the software are any help files or further explanation of the parameters available via DeNovoGUI.  While I have seen the summary (https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI#directag-advanced-parameters), I'm wondering if there may be a document you could provide with a more thorough explanation of these parameters?

Separately, when running DirecTab in DeNovoGUI, I get the following message in the progress window.

"Could not find the default configuration file (hard-coded defaults in use)."

This makes me think that it is not properly seeing the parameter settings I have configured via DeNovoGUI, even though I have updated and saved a .par file. Thanks for your input on what might be wrong here. Again I have not been able to find information on how to set up a configuration file to place within the DirecTag resource folder or to call at the command line, so any info on how to write a DirecTag params file would be helpful as well.

Thank you for your help,

Andrew

[Harald Barsnes]

Hi Andrew,

I'm afraid we've been unable to locate documentation for the DirecTag parameters as well. As you can see from the two last messages in this otherwise unrelated issue: https://github.com/compomics/searchgui/issues/173.

If you have questions about a given DirecTag parameter I'd therefore recommend contacting Matt Chambers directly.

The "Could not find the default configuration file (hard-coded defaults in use)." message can safely be ignored. But if you want to double check that your parameters are in fact used, the parameters are listed at the start of the DirecTag results file and can be inspected by a text viewer.

Best regards,

Harald