Commit d8611fd6 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

Add yaml example and how to give multiple controls to one sample

parent 8337024e
......@@ -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
......
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