The RF Wiggle module can process both RC or rf-norm output XML files to produce WIGGLE tracks. When provided with RC files, by default RF Wiggle reports the per-base raw RT-stop/mutation count.
RF Wiggle can be invoked both on individual RC/XML files, or on an entire RC/XML folders.
Multiple RC/XML files/folders can be provided at the same time.


Input file names will be stripped of their extensions, and automatically used to generate output WIGGLE files.


To list the required parameters, simply type:

$ rf-wiggle -h
Parameter Type Description
-ow or --overwrite Overwrites output file (if the specified file already exists)
-c or --coverage Reports per-base coverage instead of RT-stop/mutation count
Note: this option only works for RC files.
-r or --ratio Reports per-base ratio between RT-stop/mutation count and coverage
Note: this option only works for RC files.
-kb or --keep-bases string Bases to report in the WIG file (Default: N [ACGT])
Note: This parameter accepts any IUPAC code, or their combination (e.g. -kb M, or -kb AC). Any other base will be ignored