From b78ced98ce9ee3e5b7d8a4391a603fd864e38a2f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 9 Apr 2020 16:58:19 -0500
Subject: [PATCH] gene abund exon

---
 genect_rnaseq/geneabundance.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index 39aad28..29efd15 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -41,7 +41,7 @@ source /etc/profile.d/modules.sh
 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}
+featureCounts -s $stranded -M --fraction -J --ignoreDup -T $SLURM_CPUS_ON_NODE -t exon -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
 mkdir ${pair_id}_stringtie
 cd ${pair_id}_stringtie
 stringtie ../${sbam} -p $SLURM_CPUS_ON_NODE -G ${gtf} -B -e -o denovo.gtf -A ../${pair_id}.fpkm.txt
-- 
GitLab