From a484bedc2c6145742dfa8fffcbf6881e4d838747 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 22 May 2019 14:29:05 -0500
Subject: [PATCH] update starfusion
---
alignment/starfusion.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index dd96233..cc0d8df 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -49,7 +49,7 @@ then
mkdir $tmphome
fi
export TMP_HOME=$tmphome
- index_path=${refgeno}/CTAT_lib_trinity/
+ index_path=${refgeno}/CTAT_lib_trinity1.6
trinity /usr/local/src/STAR-Fusion/STAR-Fusion --min_sum_frags 3 --CPU $SLURM_CPUS_ON_NODE --genome_lib_dir ${index_path} --left_fq ${fq1} --right_fq ${fq2} --examine_coding_effect --output_dir ${pair_id}_star_fusion
#cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.tsv ${pair_id}.starfusion.txt
cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${pair_id}.starfusion.txt
--
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