diff --git a/docs/usage.md b/docs/usage.md index 0dccf181..bbcfaf5d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -98,14 +98,12 @@ Alternatively, the RNA premapping reference can be supplied by the user by givin By default, peak calling on identified crosslinks is not performed unless specified using the `--peakcaller` argument. Currently the following peak callers are implemented: -* [iCount](https://icount.readthedocs.io/en/latest/) - * `--peakcaller icount` -* [Paraclu](http://cbrc3.cbrc.jp/~martin/paraclu/) - * `--peakcaller paraclu` -* [PureCLIP](https://pureclip.readthedocs.io/en/latest/) - * `--peakcaller pureclip` -* [Piranha](https://github.com/smithlabcode/piranha) - * `--peakcaller piranha` +| Peak caller | Argument | Supported protocols | +|--------------------------------------------------------|-------------------------|--------------------------------------------| +| [iCount](https://icount.readthedocs.io/en/latest/) | `--peakcaller icount` | iCLIP | +| [Paraclu](https://gitlab.com/mcfrith/paraclu) | `--peakcaller paraclu` | CAGE-seq | +| [PureCLIP](https://pureclip.readthedocs.io/en/latest/) | `--peakcaller pureclip` | iCLIP, eCLIP | +| [Piranha](https://github.com/smithlabcode/piranha) | `--peakcaller piranha` | HITS-CLIP, iCLIP, eCLIP, PAR-CLIP, RIP-seq | Multiple peak callers can specified separated using a comma, e.g. `--peakcaller icount,paraclu`. As a short-hand, all peak callers can be specified using `--peakcaller all`.