From 58dc899ffc9b659815d39ac947ab7aa6f2eedab1 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 22 Jul 2020 10:25:31 -0500
Subject: [PATCH] fpkm subset bug fixed
---
genect_rnaseq/geneabundance.sh | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index 8f6f6d7..e70954a 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -11,7 +11,7 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :b:g:p:f:s:h opt
+while getopts :b:g:p:i:f:s:h opt
do
case $opt in
b) sbam=$OPTARG;;
@@ -47,14 +47,13 @@ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
featureCounts -s $stranded -M --fraction -J --ignoreDup -T $NPROC -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
-mkdir ${pair_id}_stringtie
+mkdir -p ${pair_id}_stringtie
cd ${pair_id}_stringtie
stringtie ../${sbam} -p $NPROC -G ${gtf} -B -e -o denovo.gtf -A ../${pair_id}.fpkm.txt
-
if [[ -f $filter ]]
then
cd ..
- mv ${pair_id}.fpkm.txt ${prefix}.fpkm.ori.txt
- perl ${baseDir}/fpkm_subset_panel.pl -f ${prefix}.fpkm.ori.txt -g $filter -i $ginfo
- mv ${prefix}.fpkm.capture.txt ${pair_id}.fpkm.txt
+ cp ${pair_id}.fpkm.txt ${pair_id}.fpkm.ori.txt
+ perl ${baseDir}/fpkm_subset_panel.pl -f ${pair_id}.fpkm.ori.txt -g $filter -i $ginfo
+ mv ${pair_id}.fpkm.capture.txt ${pair_id}.fpkm.txt
fi
--
GitLab