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.
Note
Input file names will be stripped of their extensions, and automatically used to generate output WIGGLE files.
Usage
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 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. |
|
| -rt or --ratio-total | Reports per-base ratio between RT-stop/mutation count and the transcript's total reads count 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 |