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
$ rf-wiggle [options] sample1.rc sample2.xml .. sampleN/
To list all available 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) |