Update compareBed.sh

bin/compareBed.sh

@@ -96,7 +96,7 @@ if [ $he == true ]
 then
 	echo "This script utilies bedtools to select new footprints from data."
 	echo "Therefore the data is compared with known footprint motifs."
-	echo "The output is a new .bed file with added sequence information."
+	echo "The output is a new .bed file with added sequence information and a column with flags for better sequences (1)"
 	echo "Required arguments are data and motifs, both in bed-format, and the fasta genome sequences."
 	echo "If a parameter is chosen, a value must be provided or an error will occur."
 	echo "--------------------"
@@ -110,7 +110,7 @@ then
 	echo "              "
 	echo "              optional parameter:"
 	echo "              -w   --workdir      the path to directory where temporary files will be created"
-	echo "                                  default is a new directory that is created in the current directory"
+	echo "                                  default is the current directory"
 	echo "              -min --min          minimum size of footprints; default is 10"
 	echo "              -max --max          maximum size of footprints; default is 80"
 	echo "              -o   --output       output path/file ; default dir is workdir and filename is newMotifs.bed and newMotifs.bed.fasta"
@@ -258,6 +258,7 @@ else
 fi
 
 #4. remove short/long motivs, make unique ids (relevant for some splitted tfbs from subtract) and handle maxScorePosition 
+# also creates a small output file with information about the comparison
 
 Rscript --vanilla /bin/merge.R $min $max "$workdir" $data