diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 055f1b5fb416a9ae8b81dcf53bde36cf06ef9549..3a5715d3bb6698133484421e12d1e5c7f6aaaa2d 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -90,6 +90,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
         "batch" -> 4,
         "format" -> "sam"
       ),
+      "cutadapt" -> Map("minimum_length" -> 20),
       // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
       "picard" -> Map(
         "programrecordid" -> "null"