I have finally successfully created the designDir files, but now had to realize that I still need more input files, including a “feature list file”, to run runChicago.R
The documentation states
en-feat-list: the name of the feature list file of the format <feature-name> <feature-bed-file-location>, where feature-bed-files contain the genomic coordinates of the features to compute the enrichment at Chicago significant interactions
(Chicago signal cutoff 5 is used by default).
I have no idea what that means. I didn't read anything about a feature list before this point (including in the 'Input files required' section of the workflow). How do I get this file, i.e. what features are meant here?