diff --git a/runBWA.sh b/runBWA.sh
new file mode 100755
index 0000000..4d796b2
--- /dev/null
+++ b/runBWA.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+module load bwa
+module load samtools
+GENOMEDIR="/work/GIF/arnstrm/GENOMEDB"
+#GNAME="Btau_4.6.1_chromosomes.fa"
+GNAME="$1"
+REF="$GENOMEDIR/$GNAME"
+THREADS="16"
+READ1="$2"
+READ2="$3"
+SAM=$(basename ${READ1%.*} | cut -f 1-2 -d "_")
+bwa mem -M -t ${THREADS} ${REF} ${READ1} ${READ2} > ${SAM}.sam
+samtools view --threads 16 -b -o ${SAM}.bam ${SAM}.sam
+samtools sort -m 8G -o ${SAM}_sorted.bam -T ${SAM}_temp --threads 16 ${SAM}.bam
diff --git a/runHISAT2.sh b/runHISAT2.sh
index 4ac8b5d..1001c50 100755
--- a/runHISAT2.sh
+++ b/runHISAT2.sh
@@ -15,7 +15,7 @@ hisat2 \
   -p ${p} \
   -x ${DBDIR}/${GENOME} \
   -1 ${R1_FQ} \
-  -2 ${R2_FQ} | \
+  -2 ${R2_FQ} \
   -S  ${OUTPUT}.sam &> ${OUTPUT}.log
 samtools view --threads 16 -b -o ${OUTPUT}.bam ${OUTPUT}.sam
 samtools sort -m 7G -o ${OUTPUT}_sorted.bam -T ${OUTPUT}_temp --threads 16 ${OUTPUT}.bam