From 8d0a5bf886305c99ccee7a94c232cf24252b9097 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <b.cantarel@gmail.com>
Date: Sat, 1 Aug 2020 17:31:07 -0500
Subject: [PATCH] Update starfusion.sh
---
alignment/starfusion.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 84deb08..a3a5099 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -59,8 +59,8 @@ then
cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate -db /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
else
refgeno=${index_path}/CTAT_resource_lib
-+ STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --CPU $NPROC --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
+ STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --CPU $NPROC --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
cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate -db agfusion.homo_sapiens.95.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
fi
--
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