From 35139bf639c88af5449dd728e677dc37d1e4fcf8 Mon Sep 17 00:00:00 2001 From: vecerkovakaterina Date: Thu, 17 Aug 2023 11:00:57 +0200 Subject: [PATCH 1/4] Add peak callers' supported protocols --- docs/usage.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 0dccf181..e62863e3 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://cbrc3.cbrc.pj.aist.go.jp/~martin/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`. From d1626d7edf125f62f4a23fc213ffbd82c7199759 Mon Sep 17 00:00:00 2001 From: vecerkovakaterina Date: Thu, 17 Aug 2023 11:01:29 +0200 Subject: [PATCH 2/4] Update link to Paraclu documentation --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index e62863e3..a6f0f73c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -101,7 +101,7 @@ By default, peak calling on identified crosslinks is not performed unless specif | Peak caller | Argument | Supported protocols | |-------------|----------|-------------------------------------------| | [iCount](https://icount.readthedocs.io/en/latest/) | `--peakcaller icount` | iCLIP | -| [Paraclu](https://cbrc3.cbrc.pj.aist.go.jp/~martin/paraclu/) | `--peakcaller paraclu` | CAGE-seq | +| [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 | From 546d1966dda38916fbe7ff3c8c8aa79f132cf85d Mon Sep 17 00:00:00 2001 From: vecerkovakaterina Date: Thu, 17 Aug 2023 11:03:08 +0200 Subject: [PATCH 3/4] Reformat table --- docs/usage.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index a6f0f73c..81838cfc 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -98,12 +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: -| 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 | +| 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 | +| [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`. From 3aaa31cdb3006760590a4793bad2e82caaaf2905 Mon Sep 17 00:00:00 2001 From: vecerkovakaterina Date: Thu, 17 Aug 2023 11:09:07 +0200 Subject: [PATCH 4/4] Add missing space character --- docs/usage.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 81838cfc..bbcfaf5d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -98,12 +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: -| 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 | +| 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`.