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.

Usage

To list the required parameters, simply type:

$ rf-wiggle -h

Parameter	Type	Description
-p or --processors	int	Number of processors (≥1, Default: 1)
-o or --output	string	Output directory (Default: rf_wiggle/)
-ow or --overwrite		Overwrites output file (if the specified file already exists)
-c or --coverage		Reports per-base coverage 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.
-mc or --min-coverage	int	Minimum coverage to report a base (requires an RC input file) (≥1, Default: 1)
-z or --report-zeroes		Bases with 0 count/ratio will be reported (if their coverage exceeds --min-coverage)
-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
-bs or --block-size	int	Defines the size of the memory block (in bp) to process RC files containing whole chromosome data (such as that generated by rf-count-genome) (≥1, Default: 1000000)