diff --git a/scripts/makeBashScripts.py b/scripts/makeBashScripts.py
index 75c5006a1b47127b305e74dbc3077942ffbdfb95..2345bbf50510884435a62b6337e3566e07017ddb 100644
--- a/scripts/makeBashScripts.py
+++ b/scripts/makeBashScripts.py
@@ -46,7 +46,7 @@ def main():
         
         script = open('bin/'  + old, 'w')
         script.write("#!/bin/sh\n")
-        script.write("bedtools " + new + " $@\n")
+        script.write("bedtools " + new + " \"$@\"\n")
         script.close()
 
 if __name__ == "__main__":