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Update peak caller documentation #101

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Add peak callers' supported protocols
vecerkovakaterina Aug 17, 2023
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Update link to Paraclu documentation
vecerkovakaterina Aug 17, 2023
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vecerkovakaterina Aug 17, 2023
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vecerkovakaterina Aug 17, 2023
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Merge branch 'dev' into master
CharlotteAnne Nov 9, 2025
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14 changes: 6 additions & 8 deletions docs/usage.md
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Expand Up @@ -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`.

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