added info, that file_paths must not contain the "|" pipe symbol

bin/1.2_filter_motifs/compareBed.sh

@@ -11,6 +11,7 @@
 #             The output is a file with the filtered footprints and the log file compareBed.stats
 
 # One R scripts is used, compareBed_runinfo.R, stored in the same directory.
+# Parameter values (file/directory paths) must not contain the | symbol, because it is chosen as "sed"-field separator.
 
 # default parameters
 workdir=$PWD
@@ -122,6 +123,8 @@ then
 	echo "              -max --max          maximum size of footprints; default is 80"
 	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.bed.fasta"
 	echo "              -h --help           shows this help message"
+	echo ""
+	echo " Note: file paths must not contain the '|' pipe symbol" 
 	exit 0
 fi