diff --git a/R/ClusteringMethods.R b/R/ClusteringMethods.R
index 9948da4..7759231 100644
--- a/R/ClusteringMethods.R
+++ b/R/ClusteringMethods.R
@@ -165,6 +165,8 @@ setMethod( "clusterCTSS", "CAGEexp"
   }
   
   CTSSclusteringMethod(ctss.cluster.list) <- method
+  seqlevels(ctss.cluster.list) <- seqlevels(CTSStagCountSE(object))
+  seqinfo(ctss.cluster.list)   <- seqinfo(CTSStagCountSE(object))
   metadata(object)$tagClusters <- ctss.cluster.list
   object
 })
diff --git a/data/exampleCAGEexp.RData b/data/exampleCAGEexp.RData
index 1c608a4..f76a8f1 100644
Binary files a/data/exampleCAGEexp.RData and b/data/exampleCAGEexp.RData differ