From d8611fd63eded4660406b8f6e9e154bb7273dc03 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 10 Mar 2016 13:58:01 +0100
Subject: [PATCH] Add yaml example and how to give multiple controls to one
sample
---
docs/pipelines/carp.md | 46 +++++++++++++++++++++++++++++++++++++++++-
1 file changed, 45 insertions(+), 1 deletion(-)
diff --git a/docs/pipelines/carp.md b/docs/pipelines/carp.md
index 1391afbf6..e6f7a498b 100644
--- a/docs/pipelines/carp.md
+++ b/docs/pipelines/carp.md
@@ -12,7 +12,9 @@ Please refer [to our mapping pipeline](mapping.md) for information about how the
### Sample Configuration
-The layout of the sample configuration for Carp is basically the same as with our other multi sample pipelines, for example:
+The layout of the sample configuration for Carp is basically the same as with our other multi sample pipelines it may be either ```json``` or ```yaml``` formatted.
+Below we show two examples for ```json``` and ```yaml```. One should appreciate that multiple libraries can be used if a sample is sequenced on multiple lanes. This is noted with library id in the config file.
+
~~~ json
{
@@ -42,8 +44,50 @@ The layout of the sample configuration for Carp is basically the same as with ou
}
~~~
+~~~ yaml
+samples:
+ sample_X
+ control:
+ - sample_Y
+ libraries:
+ lib_one:
+ R1: /absolute/path/to/first/read/pair.fq
+ R2: /absolute/path/to/second/read/pair.fq
+ sample_Y:
+ libraries:
+ lib_one:
+ R1: /absolute/path/to/first/read/pair.fq
+ R2: /absolute/path/to/second/read/pair.fq
+ lib_two:
+ R1: /absolute/path/to/first/read/pair.fq
+ R2: /absolute/path/to/second/read/pair.fq
+~~~
+
What's important here is that you can specify the control ChIP-seq experiment(s) for a given sample. These controls are usually
ChIP-seq runs from input DNA and/or from treatment with nonspecific binding proteins such as IgG. In the example above, we are specifying `sample_Y` as the control for `sample_X`.
+**Please notice** that the control is given in the form of a ```list```. This is because sometimes one wants to use multiple control samples, this can be achieved to pass the sampleNames of the control samples in a list to the field **control** in the config file.
+In ```json``` this will become:
+
+~~~ json
+{
+ "samples": {
+ "sample_X": {
+ "control": ["sample_Y","sample_Z"]
+ }
+ }
+ }
+ ~~~
+
+In ```yaml``` this is a bit different and will look like this:
+
+~~~ yaml
+samples:
+ sample_X:
+ control:
+ - sample_Y
+ - sample_Z
+~~~
+
### Pipeline Settings Configuration
--
GitLab