Figure 6.

Layout of folders for running script for compilation of data

(A) A parent folder (here called ‘Cys-LOx example’) contains a folder called ‘data,’ which contains subfolders of the two conditions (NT = no treatment, LPS = LPS + IFNγ). Each experimental condition subfolder contains the FragPipe output folders for each corresponding replicate. The parent folder also contains the Python script file (here called ‘230119_mouse_process’) and all the additional FragPipe output files.

(B) Contents of the ‘results’ file that is generated upon execution of the command in step 3d. The ‘compiled_identifiers.tsv’ output is loaded directly into Perseus for further processing.