Commit 8eb7deef authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'docs-carp-broadpeaks' into 'develop'

ATAC seq config

@s.a.j.van_der_zeeuw kun je even kijken of er nog iets mist?

See merge request !425
parents 196fc34e e2786185
......@@ -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]( 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
"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
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