diff --git a/gene-counts.sh b/gene-counts.sh
new file mode 100644
index 0000000000000000000000000000000000000000..8b6855e5669e4cd86c9bda7884768b5e589fdde4
--- /dev/null
+++ b/gene-counts.sh
@@ -0,0 +1,93 @@
+#!/bin/bash
+# gene-counts.sh
+
+script_name="gene-counts.sh"
+script_ver="1.0.0"
+
+#Help function
+usage() {
+ echo "-h Help documentation for $script_name"
+ echo "-a --Path to bam file"
+ echo "-b --Path to bam file2"
+ echo "-g --Path to the annotation file"
+ echo "-o --Path to output directory"
+ echo "-e --The experiment names."
+ echo "-v --Version of script"
+ echo "Example: $script_name -a 'foo_1.bam' -b 'foo_2.bam' -g '/path/to/gtf/gencode.v19.annotation.gtf' [-o '/path/to/output/dir/']"
+ exit 1
+}
+
+# Version function
+version(){
+ echo "$script_name $script_ver"
+ exit 1
+}
+
+main(){
+
+
+ # Load required modules
+ module load RSEM/1.2.31
+ module load python/2.7.x-anaconda
+ module load picard/1.127
+
+ # Parsing options
+ OPTIND=1 # Reset OPTIND
+ while getopts :a:b:s:g:e:o:vh opt
+ do
+ case $opt in
+ a) aln_file_2=$OPTARG;;
+ b) aln_file_1=$OPTARG;;
+ g) transcriptome=$OPTARG;;
+ e) exp=$OPTARG;;
+ o) out=$OPTARG;;
+ v) version;;
+ h) usage;;
+ esac
+ done
+
+ shift $(($OPTIND -1))
+
+ # Check for mandatory options
+ if [[ -z $aln_file_1 ]] || [[ -z $aln_file_2 ]] || [[ -z $transcriptome ]] || [[ -z $exp ]]; then
+ usage
+ fi
+
+ # Define the output directory, if none defined make the location relative to first file
+ if [ -z $out ]; then
+ one_parent=$(dirname "${aln_file_1}")
+ out_dir=$(dirname "${one_parent}")\/$script_name-$script_ver/
+ else
+ out_dir=$out\/$script_name-$script_ver
+ fi
+
+ if [ ! -d $out_dir ]; then
+ mkdir $out_dir
+ fi
+
+
+ # If filtered alignment file doesn't exist
+ if [ ! -e $out_dir/$exp.counts ]; then
+
+
+ java -Xmx2g -jar $PICARD/picard.jar MergeSamFiles OUTPUT=$out_dir/$exp.bam INPUT=$aln_file_1 INPUT=$aln_file_2
+
+ rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000 $out_dir/$exp.bam $transcriptome $out_dir/$output_fp
+
+ rm $out_dir/$exp.bam
+
+ # Get input and output files and then print out metadata.json file
+ input_files=("$aln_file_1", "$aln_file_2", "$transcriptome")
+ printf -v input "\"%s\"," "${input_files[@]}"
+ input=${input%,}
+ output_file=($out_dir/$output_fp*)
+ printf -v output "\"%s\"," "${output_file[@]}"
+ output=${output%,}
+ printf '{"script name":"%s","script version":"%s", "input files": [%s], "output files": [%s]}' "$script_name" "$script_ver" "$input" "$output" | python -m json.tool > $out_dir/$output_fp.metadata.json
+
+ else
+ echo "* Counts have already been called for $raw_fn"
+ fi
+}
+
+main "$@"
diff --git a/make-normal-signal.sh b/make-normal-signal.sh
new file mode 100755
index 0000000000000000000000000000000000000000..cad6caf5e410875eb389662cd72150eedcfbbe63
--- /dev/null
+++ b/make-normal-signal.sh
@@ -0,0 +1,93 @@
+#!/bin/bash
+# make-normal-signal.sh
+
+script_name="make-normal-signal.sh"
+script_ver="1.0.0"
+
+#Help function
+usage() {
+ echo "-h Help documentation for $script_name"\\n
+ echo "-f --File path to Replicate 1 alignment."
+ echo "-s --File path to Replicate 2 alignment."
+ echo "-r --UCSC Reference genome (e.g. hg19, mm10)"
+ echo "-e --The experiment names."
+ echo "-o --The ouput directory."
+ echo "Example: $script_name -f 'foo1.bam' -s 'foo2.bam man2.bam' -r 'hg19' -e 'foo man' -o output"
+ exit 1
+}
+
+# Version function
+version(){
+ echo "$script_name $script_ver"
+ exit 1
+}
+
+main(){
+
+ # Load required modules
+ module load python/2.7.x-anaconda
+ module load star/2.4.2a
+ module load picard/1.127
+ module load UCSC_userApps/v317
+
+ # Parsing options
+ OPTIND=1 # Reset OPTIND
+ while getopts :f:s:r:e:o:hv opt
+ do
+ case $opt in
+ f) aln1=$OPTARG;;
+ s) aln2=$OPTARG;;
+ r) ucsc_reference=$OPTARG;;
+ e) exp=$OPTARG;;
+ o) out=$OPTARG;;
+ h) usage;;
+ v) version;;
+ esac
+ done
+
+ shift $(($OPTIND -1))
+
+ # Check for mandatory options
+ if [[ -z $aln1 ]] || [[ -z $aln2 ]] || [[ -z $ucsc_reference ]] || [[ -z $exp ]] || [[ -z $out ]]; then
+ usage
+ fi
+
+ # Define the out directory
+ out_dir=$out\/$script_name-$script_ver
+
+ # Make sure directories exist
+ if [ ! -e $out ]; then
+ mkdir $out
+ fi
+
+ # Run make-normal-signal.R if directory doesn't exist
+ if [ ! -d $out_dir ]; then
+ mkdir $out_dir
+ # Fetch chrom sizes
+ echo "* Downloading chrom.sizes..."
+ fetchChromSizes $ucsc_reference > $out_dir/chrom.sizes
+
+ java -Xmx2g -jar $PICARD/picard.jar MergeSamFiles OUTPUT=$out_dir/$exp.bam INPUT=$aln1 INPUT=$aln2
+ cd $out_dir
+ STAR --runMode inputAlignmentsFromBAM --inputBAMfile $exp.bam --outWigType bedGraph --outWigStrand Stranded --outFileNamePrefix $exp --outWigReferencesPrefix chr
+ bedSort $out_dir/$exp\Signal.UniqueMultiple.str1.out.bg $out_dir/$exp\Signal.UniqueMultiple.str1.out.sorted.bg
+ bedSort $out_dir/$exp\Signal.UniqueMultiple.str2.out.bg $out_dir/$exp\Signal.UniqueMultiple.str2.out.sorted.bg
+ bedGraphToBigWig $out_dir/$exp\Signal.UniqueMultiple.str1.out.sorted.bg $out_dir/chrom.sizes $out_dir/$exp.negative.bw
+ bedGraphToBigWig $out_dir/$exp\Signal.UniqueMultiple.str2.out.sorted.bg $out_dir/chrom.sizes $out_dir/$exp.positive.bw
+ rm $out_dir/$exp*.bg
+ rm $out_dir/$exp.bam
+
+ # Get input and output files and then print out metadata.json file
+ input_files=("${array_aln1[@]}" "${array_aln2[@]}")
+ printf -v input "\"%s\"," "${input_files[@]}"
+ input=${input%,}
+ output_file=($out_dir\/*)
+ printf -v output "\"%s\"," "${output_file[@]}"
+ output=${output%,}
+ printf '{"script name":"%s","script version":"%s", "input files": [%s], "output files": [%s]}' "$script_name" "$script_ver" "$input" "$output" | python -m json.tool > $out_dir/metadata.json
+ else
+ echo "* Normalized Signal has been made. "
+ fi
+}
+
+main "$@"