From 50e51be873af153c58f026e46d02f1b329ecfb5e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 8 Jan 2019 17:11:32 -0600
Subject: [PATCH] adding options to export junction file
---
diff_exp/geneabundance.sh | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/diff_exp/geneabundance.sh b/diff_exp/geneabundance.sh
index 40a68ab..1baa572 100644
--- a/diff_exp/geneabundance.sh
+++ b/diff_exp/geneabundance.sh
@@ -39,8 +39,7 @@ then
fi
source /etc/profile.d/modules.sh
module load subread/1.6.1 stringtie/1.3.2d-intel
-featureCounts -s $stranded -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 -p -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
--
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