Table 1. Flexible user-defined cuRRBS parameters.
| cuRRBS parameter (abbrev.) | Significance | Default | Range |
|---|---|---|---|
| Enzymes to check (-e) | Defines the enzymes (isoschizomer families) that cuRRBS will look at | - | - |
| Annotation for the sites of interest (-a) | Allows identification and weighting of the sites of interest | - | - |
| Read length (-r) | Defines the positions in the theoretical fragments that can be ‘seen’ after sequencing | - | 30–300 |
| Adapters size (-s) | Ensures correct experimental size selection | - | - |
| C_Score constant (-c) | Sets the minimum acceptable Score | - | 0–1 |
| Genome size (-g) | Needed to calculate the CRF | - | - |
| C_NF/1000 constant (-k) | Sets the minimum acceptable CRF | 0.2 | 0–1 |
| Experimental error (-d) | Sets the assumed experimental error (δ) | 20 | 5–500 |
| Size range breadth (-b) | Constrains the breadth of the size range | 980 | - |
| Output size (-t) | Defines the number of cuRRBS protocols the user can compare | 30 | - |
| Site IDs (-i) | Enables the identification of the recovered sites of interest | No | - |
This table details the flexible user-defined parameters that cuRRBS will accept as arguments. The cuRRBS parameter full name and command-line abbreviation (in brackets) are provided alongside a simplified description of the significance of these arguments to the user. Where applicable, the defaults and ranges are also detailed.