diff --git a/docs/pipelines/carp.md b/docs/pipelines/carp.md index f3e1f31b3579a228a2240c7476dfc9a687a039d5..436bd7e48c5803a14afc552e93667eb159a1ef64 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