diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
index e1b94b874d69fc19c684b0f7792364874e6d3f33..96abaf1edb0725c21f8e1d41a698438b13f74d4f 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
@@ -85,7 +85,8 @@ object MergeTables {
             idCols: List[Int],
             valCol: Int,
             numHeaderLines: Int = 0,
-            fallback: String = "-"): MergeTables = {
+            fallback: String = "-",
+            fileExtension: Option[String] = None): MergeTables = {
     val job = new MergeTables(root)
     job.inputTables = tables
     job.output = outputFile
@@ -93,6 +94,7 @@ object MergeTables {
     job.valueColumnIndex = valCol
     job.fallbackString = Option(fallback)
     job.numHeaderLines = Option(numHeaderLines)
+    job.fileExtension = fileExtension
     job
   }
 }
\ No newline at end of file
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 8bfc3158e672f5b4b25a39514367e3c53385040f..a88563eb817a2e9d058d5ba4255e6cc86e2bdf42 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -307,7 +307,7 @@ object BaseCounter extends ToolCommand {
     val exonCounts = transcript.exons.map(new RegionCount(_))
     val intronCounts = if (transcript.exons.size > 1)
       intronRegions.allRecords.map(e => new RegionCount(e.start + 1, e.end)).toList
-      else Nil
+    else Nil
     def addRecord(samRecord: SAMRecord, sense: Boolean): Unit = {
       bamRecordBasesOverlap(samRecord, transcript.start, transcript.end, counts, sense)
       exonCounts.foreach(_.addRecord(samRecord, sense))
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 3ad9146b62648aa438f407f4c6e47b0bcaf00f73..98d1aeed37b4585f0991674b8d6c28755933ba5b 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
@@ -29,7 +29,7 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
     def addTableAndHeatmap(countFiles: List[File], outputName: String): Unit = {
       val mergedTable = new File(outputDir, s"$name.$outputName.tsv")
       val heatmapFile = new File(outputDir, s"$name.$outputName.png")
-      addMergeTableJob(countFiles, mergedTable, outputName)
+      addMergeTableJob(countFiles, mergedTable, outputName, countFiles.head.getName.stripPrefix(jobs.head._1))
       addHeatmapJob(mergedTable, heatmapFile, outputName)
     }
 
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
index d1cf59fdd666e854fdd7212401145fb444295b2f..2d4f40973c0e1b319de354e23f16de0dc594826b 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
@@ -1,6 +1,6 @@
 package nl.lumc.sasc.biopet.pipelines.gentrap.measures
 
-import nl.lumc.sasc.biopet.extensions.Cufflinks
+import nl.lumc.sasc.biopet.extensions.{ Ln, Cufflinks }
 import nl.lumc.sasc.biopet.extensions.tools.MergeTables
 import org.broadinstitute.gatk.queue.QScript
 
@@ -23,8 +23,22 @@ trait CufflinksMeasurement extends QScript with Measurement {
         id -> cufflinks
     }
 
-    addMergeTableJob(jobs.values.map(_.outputGenesFpkm).toList, mergeGenesFpkmTable, "genes_fpkm")
-    addMergeTableJob(jobs.values.map(_.outputIsoformsFpkm).toList, mergeIsoFormFpkmTable, "iso_form")
+    val genesFpkmFiles = jobs.toList.map {
+      case (id, job) =>
+        val file = new File(job.output_dir, s"$id.genes_fpkm.counts")
+        add(Ln(this, job.outputGenesFpkm, file))
+        file
+    }
+
+    val isoFormFpkmFiles = jobs.toList.map {
+      case (id, job) =>
+        val file = new File(job.output_dir, s"$id.iso_form_fpkn.counts")
+        add(Ln(this, job.outputIsoformsFpkm, file))
+        file
+    }
+
+    addMergeTableJob(genesFpkmFiles, mergeGenesFpkmTable, "genes_fpkm", ".genes_fpkm.counts")
+    addMergeTableJob(isoFormFpkmFiles, mergeIsoFormFpkmTable, "iso_form_fpkn", ".iso_form_fpkn.counts")
 
     addHeatmapJob(mergeGenesFpkmTable, genesFpkmHeatmap, "genes_fpkm")
     addHeatmapJob(mergeIsoFormFpkmTable, isoFormFpkmHeatmap, "iso_form_fpkm")
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index a383874f16a2699922dd9fccb48b7a4ac274b331..9ed01b496e537a779b4cd494e6424818ce063f7a 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -20,7 +20,7 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
         val job = new HtseqCount(this)
         job.inputAnnotation = annotationGtf
         job.inputAlignment = file
-        job.output = new File(outputDir, s"$name.$id.counts")
+        job.output = new File(outputDir, s"$id.$name.counts")
         job.format = Option("bam")
         add(job)
         // We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
@@ -30,7 +30,7 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
         id -> job
     }
 
-    addMergeTableJob(jobs.values.map(_.output).toList, mergedTable, "fragments_per_gene")
+    addMergeTableJob(jobs.values.map(_.output).toList, mergedTable, "fragments_per_gene", s".$name.counts")
     addHeatmapJob(mergedTable, heatmap, "fragments_per_gene")
   }
 
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
index 095a01fdbb5ddf2024198dc01f11bd79b89c53de..768fa98b1715828944156102ae5e3fcd72180058 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
@@ -41,6 +41,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
   def addMergeTableJob(countFiles: List[File],
                        outputFile: File,
                        name: String,
+                       fileExtension: String,
                        args: MergeArgs = mergeArgs): Unit = {
     add(MergeTables(this, countFiles, outputFile,
       args.idCols, args.valCol, args.numHeaderLines, args.fallback))