diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index e1ac62f..99423f7 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -89,7 +89,7 @@ case $key in
 esac
 done
 
-# stores unknown selected parameters for error report 
+# stores unknown selected parameters for error report
 count=${#wrong[@]}
 if [ $count -gt 0 ]
 then
@@ -178,7 +178,7 @@ then
 fi
 
 #default path of the scripts merge.R and maxScore.R is the same path as compareBed.sh has
-# the `echo $0 | sed 's/\/[^\/]*$/\//g'` command extracts the path from $0, where the command itself is stored 
+# the `echo $0 | sed 's/\/[^\/]*$/\//g'` command extracts the path from $0, where the command itself is stored
 if [ $pa == false ]
 then
 	path=`echo $0 | sed 's/\/[^\/]*$/\//g'`
@@ -198,6 +198,7 @@ if [ -d "$motifs" ]
 then
 for i in "$motifs"/*.bed
 do
+	sed -i 's/[ \t]*$//' $i
 	if [ $help == true ]
 	then
 		help=false
@@ -272,7 +273,7 @@ do
 done
 fi
 
-#The output of the last iteration of the subtract loop is written to pass2Tr.bed 
+#The output of the last iteration of the subtract loop is written to pass2Tr.bed
 if [ $help == false ]
 then
 	cat "$workdir"/pass1FaHelp.bed > "$workdir"/pass2Tr.bed