diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index 7cf0017..2c4c9ba 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -176,7 +176,8 @@ then
 	echo "directory $workdir does not exist. Please check parameter -w / --workdir"
 	exit 1
 fi
-if [[ ${output: -4: -1} != '.bed' ]]
+# check if output path ends with .bed. If not, the filename is extended by ".bed"
+if [[ ${output: -4} != '.bed' ]]
 then
 	output=`echo $output | sed "s|$|.bed|g"`
 fi