Yaamini’s Notebook: PECAN Update 4

Reformatting PECAN inputs

Jupyter notebook found here

After comapring my PECAN inputs with Laura’s we realized that I had been using the undigested proteome as a database this whole time! I had the digested file, but just didn’t use it. To remedy this, I did the folliwng (see Jupyter notebook for explicit details):

  • Converted the digested proteome to a .tabular file format
  • Removed extraneous columns from my .tabular digested proteome (needed only the “Protein Name” and “Sequence” columns
  • Updated the file path in my background proteome path list
  • Selected 5 samples to analyze
  • Updated mzML file path list
  • Uploaded all PECAN inputs to OWL
  • Downloaded folder from OWL into Documents directory on Roadrunner

Everything is now set up for Sean to run the code!

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