large delta masses in PSMs marked "narrow" instead of "open"

[mriffle]

I am running the latest CONGA on comet data.

Previously when I ran CONGA, I would see large values (values greater than 1) for the delta_mass column in the conga.target.txt in PSMs marked as "open". However, when running CONGA now, I am seeing no values > 1 for PSMs marked as "open", but am seeing such values for PSMs marked "narrow"--which I never did before.

For example:

1.87e-15        294.226 IISNASCTTNCLAPLAK       1.0     narrow  2       2013.095554     72061   sp|P04406|G3P_HUMAN

Has a bug been introduced that is switching these labels?

[freejstone]

Hi Mike. I wasn't able to reproduce the same issue using the comet search files under the data folder. Is it possible that you are giving CONGA the open-search file first and then the narrow-search file after? CONGA requires the first file input to be the narrow one, then the open one.

[mriffle]

Aha, that's it! Thanks! Though this does make me wonder if those should be parameters like --wide_results and --narrow_results or something.

[freejstone]

Yeah I like that idea, I will make the change at some point.