From 01a5af0a742ad7f3d8b2be7da771134d5bd197fb Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 21 Oct 2019 11:33:31 -0500
Subject: [PATCH] update stringtie b/c of gtf parsing error
---
genect_rnaseq/geneabundance.sh | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index e763ef7..39aad28 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -38,7 +38,9 @@ then
SLURM_CPUS_ON_NODE=64
fi
source /etc/profile.d/modules.sh
-module load subread/1.6.1 stringtie/1.3.2d-intel
+module load subread/1.6.1
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
+
featureCounts -s $stranded -M --fraction -J --ignoreDup -T $SLURM_CPUS_ON_NODE -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
mkdir ${pair_id}_stringtie
cd ${pair_id}_stringtie
--
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