--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts2bed.sh	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,78 @@
+#!/bin/bash
+
+# featurecounts2bed - converts featureCounts output to BED format
+
+# Copyright 2013-2014, Youri Hoogstrate
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License at <http://www.gnu.org/licenses/> for
+# more details.
+
+# This tool has been written by Youri Hoogstrate from the Erasmus
+# Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+# Research IT (TraIT) project:
+# http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+# 
+# More tools by the Translational Research IT (TraIT) project can be
+# found in the following repository:
+# http://toolshed.dtls.nl/
+
+
+exon_level="true"
+filename=""
+
+# Parse parameters
+while getopts e:f: option
+do
+	case "${option}"
+	in
+		e) exon_level=${OPTARG};;
+		f) filename=$OPTARG;;
+	esac
+done
+
+# Convert the file
+if [ $filename == "" ]; then
+	echo "Usage:"
+	echo "  -e [true, false]   true = entry for every exon; false = line for genes first exon"
+	echo "  -f                 FILENAME from featureCounts"
+else
+	while read line; do
+		first=${line:0:1}
+		if [ $first != "#" ]; then
+			columns=($line)
+			uid=${columns[@]:0:1}
+			if [ $uid != "Geneid" ]; then
+				chr=${columns[@]:1:1}
+				start=${columns[@]:2:1}
+				stop=${columns[@]:3:1}
+				direction=${columns[@]:4:1}
+				length=${columns[@]:5:1}
+				count=${columns[@]:6:1}
+				
+				chr_splitted=($(echo $chr | tr ";" "\n"))
+				start_splitted=($(echo $start | tr ";" "\n"))
+				stop_splitted=($(echo $stop | tr ";" "\n"))
+				strand_splitted=($(echo $direction | tr ";" "\n"))
+				
+				if [ $exon_level == "true" ]; then
+					n=${#chr_splitted[@]}
+				else
+					n=1
+				fi
+				
+				for (( i=0; i<$n; i++ ))
+				do
+					echo ${chr_splitted[@]:$i:1}"	"${start_splitted[@]:$i:1}"	"${stop_splitted[@]:$i:1}"	"$uid" ("$((${stop_splitted[@]:$i:1}-${start_splitted[@]:$i:1}))"/"$length"nt)	"$count"	"${strand_splitted[@]:$i:1}
+				done
+			fi
+		fi
+	done < $filename
+fi