--- a +++ b/docs/commandline.rst @@ -0,0 +1,33 @@ +================== +Command line tools +================== + +:code:`janggu` +--------------------- + +The janggu app can be used to browse +through the results of one or more models using +webbrowser of your choice. + +Example usage:: + + janggu -path <results-root> -port <PORT> + + +:code:`janggu-trim` +------------------- + +janggu-trim can be used to trim the interval starts +and ends of a given BED/GFF file which is intended +for creating the ROI by a specified factor. + +Trimming might circumvent undesired round effects when +using :code:`resolution>1` and :code:`store_whole_genome=True` +to handle covarage data with :code:`Cover`. +Therefore, we suggest to trim the ROIs that are used during +training and evaluation beforehand. For the sake of convenience, +we added the tool janggu-trim to do that. + +Example usage:: + + janggu-trim input.bed trimmed.bed -divby 50