From e27861850e7a3ec8978131d4832934d7aa05c4a4 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 20 Jun 2016 13:23:39 +0200
Subject: [PATCH] ATAC seq config
---
docs/pipelines/carp.md | 24 +++++++++++++++++++++++-
1 file changed, 23 insertions(+), 1 deletion(-)
diff --git a/docs/pipelines/carp.md b/docs/pipelines/carp.md
index f3e1f31b3..436bd7e48 100644
--- a/docs/pipelines/carp.md
+++ b/docs/pipelines/carp.md
@@ -76,7 +76,7 @@ In ```json``` this will become:
}
}
}
- ~~~
+~~~
In ```yaml``` this is a bit different and will look like this:
@@ -101,6 +101,28 @@ While optional settings are:
1. `aligner`: which aligner to use (`bwa` or `bowtie`)
2. `macs2`: Here only the callpeak modus is implemented. But one can set all the options from [macs2 callpeak](https://github.com/taoliu/MACS/#call-peaks) in this settings config. Note that the config value is: `macs2_callpeak`
+## Configuration for detection of broad peaks (ATAC-seq)
+
+Carp can do broad peak-calling by using the following config:
+
+``` json
+ "bowtie2": {
+ "maxins": 2000,
+ "m": 1
+ },
+
+ "macs2callpeak":{
+ "gsize": 1.87e9,
+ "bdg": true,
+ "nomodel": true,
+ "broad": true,
+ "extsize": 200,
+ "shift": 100,
+ "qvalue": 0.001
+ }
+```
+
+These settings are optimized to call peaks on samples prepared using the ATAC protocol.
## Running Carp
--
GitLab