diff --git a/conf/modules.config b/conf/modules.config
index c1e552d5..901957d9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -352,7 +352,8 @@ process {
         --alignInsertionFlush Right \
         --alignSplicedMateMapLminOverLmate 0 \
         --alignSplicedMateMapLmin 30 \
-        --chimOutType Junctions'
+        --chimOutType Junctions \
+        --quantMode GeneCounts'
     }
 
     withName: STAR_GENOMEGENERATE {