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CaronLab / MhcVizPipe

A reporting pipeline for visualization of immunopeptidomics MS data.
MIT License
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Changing peptide length filter #10

Open DavidGZ1 opened 2 years ago

DavidGZ1 commented 2 years ago

Hi,

Is it possible to change the filter for peptide length for predictions ? Although the default (8 to 12 residues) can work well for some allotypes, others may include shorter or larger peptides (e.g. 7 to 13 residues).

Thanks for the great work on MhcVizPipe!

Best wishes, David

kevinkovalchik commented 2 years ago

Hi David,

Thanks for your interest in the tool. There are some limitations here, because we run everything through NetMHCpan and it has a minimum length requirement of 8 residues. This is something we might get around eventually by including other prediction tools...

However, there isn't anything preventing us from allowing the user to change the maximum length. Would that be useful enough to you on its own?

Best wishes, Kevin

DavidGZ1 commented 2 years ago

Hi Kevin, Thanks for your reply. Yes, being able to include peptides with up to 13 amino acids would be very helpful for us. Best wishes, David

kevinkovalchik commented 2 years ago

Hi David,

Okay, sounds good. I will look into implementing this. Most likely it will end up in the settings popup window. If you think it would be more useful to have it as an option in the main GUI I can look into that (e.g. if you need to change it often), but it would be easier to put it in the settings.

Best, Kevin

DavidGZ1 commented 2 years ago

Hi Kevin, I think that having the option in the settings popup would be the best. Thanks a lot! Best, David

kevinkovalchik commented 2 years ago

Hi David,

I just released a new version that should take care of this. You can update MhcVizPipe from within the GUI. You'll then need to update the settings, since the parameter was not present in the previous version. To do so, open the settings window and click the "LOAD DEFAULTS" button. This will add two parameters under the ANALYSIS section: class I max length and class II max length.

Sorry for the slow update on my part. COVID made its way into the household a couple weeks ago and everything has slowed down for a while...

Let me know if the new update works for you.

Best wishes, Kevin

DavidGZ1 commented 2 years ago

Hi Kevin, Thanks a lot for adapting the settings to include larger peptides, that worked perfectly! Sorry also for my very late reply. I tested that in a hurry and then forgot to update you. I hope that you recovered completely from COVID and everything goes fine for you. Best wishes, David