diff --git a/config/config.yaml b/config/config.yaml
index 2c920de03b30a762588fbbeb9389f7d607aa80c8..86e8f3f451fb48b06db7dab6dae2c7e79e8fe780 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -168,7 +168,7 @@ feature_counts:
 bamCoverage:
     do: yes
     options: "--filterRNAstrand forward --effectiveGenomeSize 2913022398 --normalizeUsing RPKM" 
-
+    threads: 4
 
 
 #===============================================================================
diff --git a/workflow/rules/bamCoverage.rules b/workflow/rules/bamCoverage.rules
index 7c6167f91010f1056febf3c59d1abe73a8a42d35..535b8d577180782dec0668dcff16dca03dfad558 100755
--- a/workflow/rules/bamCoverage.rules
+++ b/workflow/rules/bamCoverage.rules
@@ -36,9 +36,11 @@ rule bamCoverage:
         options = bamCoverage_options
     envmodules:
         "deepTools"
+    threads:
+        config['bamCoverage']['threads']
     shell:
         """
-        bamCoverage --bam {input} --outFileName {output} {params.options} 2> {log}
+        bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log}
         """