added run gsnap script

ISUgenomics · Feb 21, 2017 · 8073a71 · 8073a71
1 parent bfbf9cd
commit 8073a71
Showing 1 changed file with 18 additions and 0 deletions.
diff --git a/runGSNAP.sh b/runGSNAP.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+GMAPDB="/work/GIF/arnstrm/GENOMEDB"
+DB_NAME="Gmax_275_v2.0_gsnap"
+R1="$1"
+R2="$2"
+OUTFILE=$(basename ${R1} |cut -f 1 -d "_")
+gsnap \
+   -d ${DB_NAME} \
+   -D ${GMAPDB}
+   -t 16 \
+   -B 5 \
+   -N 1
+   -m 5 \
+   --gunzip \
+   --fails-as-input \
+   --input-buffer-size=10000000 \
+   --output-buffer-size=10000000 \
+   -A_gsnap.sam  ${R1} ${R2} > ${OUTFILE}_gsnap_gsnap.sam