From 735e89ceda1953e1d48f7d6963facb2e2caece84 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 12 Oct 2018 16:55:37 -0500
Subject: [PATCH] update star fusion
---
alignment/starfusion.sh | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index b999346..27937e8 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -50,14 +50,14 @@ then
fi
export TMP_HOME=$tmphome
index_path=${refgeno}/CTAT_lib_trinity/
- 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 star_fusion
- cp star_fusion/star-fusion.fusion_predictions.abridged.tsv ${pair_id}.starfusion.txt
- cp star_fusion/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${pair_id}.starfusion.coding_effect.txt
+ 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 ${pair_id}.starfusion.coding_effect.txt
else
module add star/2.5.2b
index_path=${refgeno}/CTAT_lib/
- STAR-Fusion --genome_lib_dir ${index_path} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir star_fusion &> star_fusion.err
- cp star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
+ STAR-Fusion --genome_lib_dir ${index_path} --min_sum_frags 3 --left_fq ${fq1} --right_fq ${fq2} --output_dir ${pair_id}_star_fusion &> star_fusion.err
+ cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
fi
if [[ $filter==1 ]]
then
--
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