From f866383d66f780d98de2c1267703b4d3473f6250 Mon Sep 17 00:00:00 2001 From: nchernia Date: Tue, 12 May 2020 14:31:38 -0400 Subject: [PATCH] Update juicer.sh --- UGER/scripts/juicer.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/UGER/scripts/juicer.sh b/UGER/scripts/juicer.sh index 424ec9b..af7f987 100755 --- a/UGER/scripts/juicer.sh +++ b/UGER/scripts/juicer.sh @@ -252,6 +252,7 @@ then DpnII) ligation="GATCGATC";; MboI) ligation="GATCGATC";; NcoI) ligation="CCATGCATGG";; + Arima) ligation="'(GAATAATC|GAATACTC|GAATAGTC|GAATATTC|GAATGATC|GACTAATC|GACTACTC|GACTAGTC|GACTATTC|GACTGATC|GAGTAATC|GAGTACTC|GAGTAGTC|GAGTATTC|GAGTGATC|GATCAATC|GATCACTC|GATCAGTC|GATCATTC|GATCGATC|GATTAATC|GATTACTC|GATTAGTC|GATTATTC|GATTGATC)'";; none) ligation="XXXX";; *) ligation="XXXX" echo "$site not listed as recognized enzyme. Using $site_file as site file" @@ -512,7 +513,7 @@ SPLITEND fi touchfile=${tmpdir}/${jname} - myjid=$(qsub -terse -o ${debugdir}/count_ligations-${groupname}-${jname}.out -e ${debugdir}/count_ligations-${groupname}-${jname}.err -q ${queue} -r y -l h_rt=${queue_time} -N ${groupname}${jname}countligations -v usegzip=${usegzip},name=${name},name1=${name1},name2=${name2},ext=${ext},ligation=${ligation} ${juiceDir}/scripts/countligations.sh) + myjid=$(qsub -terse -o ${debugdir}/count_ligations-${groupname}-${jname}.out -e ${debugdir}/count_ligations-${groupname}-${jname}.err -q ${queue} -r y -l h_rt=${queue_time} -N ${groupname}${jname}countligations -v usegzip=${usegzip},name=${name},name1=${name1},name2=${name2},ext=${ext},ligation="${ligation}" ${juiceDir}/scripts/countligations.sh) echo "Count ligations $jname job $myjid" >> ${debugdir}/jobs-${groupname}.out if [ -z $chimeric ] then