diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
index 05a3025efb2372ec057a1d07456064b8c9aef6f7..16348d31b6e88374a5622e48180a380af4fa94af 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
@@ -71,6 +71,10 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
   def mergeIntronCounts = new File(outputDir, s"$prefix.base.intron.merge.counts")
   def mergeIntronSenseCounts = new File(outputDir, s"$prefix.base.intron.merge.sense.counts")
   def mergeIntronAntiSenseCounts = new File(outputDir, s"$prefix.base.intron.merge.antisense.counts")
+  def nonStrandedMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.non_stranded.counts")
+  def strandedMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.counts")
+  def strandedSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.sense.counts")
+  def strandedAntiSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.antisense.counts")
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
@@ -83,7 +87,9 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
       geneExonicCounts, geneExonicSenseCounts, geneExonicAntiSenseCounts,
       geneIntronicCounts, geneIntronicSenseCounts, geneIntronicAntiSenseCounts,
       mergeExonCounts, mergeExonSenseCounts, mergeExonAntiSenseCounts,
-      mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts)
+      mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts,
+      nonStrandedMetaExonCounts,
+      strandedMetaExonCounts, strandedSenseMetaExonCounts, strandedAntiSenseMetaExonCounts)
   }
 
   override def cmdLine = super.cmdLine +
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
index 98d1aeed37b4585f0991674b8d6c28755933ba5b..d54fc2b3331446c1ab47756a5aaa93b3564649d5 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
@@ -63,5 +63,9 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
     addTableAndHeatmap(jobs.values.map(_.mergeIntronCounts).toList, "mergeIntronCounts")
     addTableAndHeatmap(jobs.values.map(_.mergeIntronSenseCounts).toList, "mergeIntronSenseCounts")
     addTableAndHeatmap(jobs.values.map(_.mergeIntronAntiSenseCounts).toList, "mergeIntronAntiSenseCounts")
+    addTableAndHeatmap(jobs.values.map(_.nonStrandedMetaExonCounts).toList, "nonStrandedMetaExonCounts")
+    addTableAndHeatmap(jobs.values.map(_.strandedMetaExonCounts).toList, "strandedMetaExonCounts")
+    addTableAndHeatmap(jobs.values.map(_.strandedSenseMetaExonCounts).toList, "strandedSenseMetaExonCounts")
+    addTableAndHeatmap(jobs.values.map(_.strandedAntiSenseMetaExonCounts).toList, "strandedAntiSenseMetaExonCounts")
   }
 }