From d4013ee37b788df42904e5ca24f723d8af430876 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 10 Apr 2018 11:28:25 -0500
Subject: [PATCH] adding updates for rna
---
alignment/rnaseqalign.sh | 4 ++--
diff_exp/geneabundance.sh | 2 +-
variants/germline_vc.sh | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index b86be37..0ed4036 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -55,9 +55,9 @@ else
module load hisat2/2.1.0-intel
if [ $fq1 == $fq2 ]
then
- hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --add-chrname --no-unal --dta -x ${index_path}/hisat_index/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
+ hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
else
- hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --add-chrname --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
+ hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
fi
if [[ $umi==1 ]]
then
diff --git a/diff_exp/geneabundance.sh b/diff_exp/geneabundance.sh
index bc54feb..0bf9535 100644
--- a/diff_exp/geneabundance.sh
+++ b/diff_exp/geneabundance.sh
@@ -34,7 +34,7 @@ then
SLURM_CPUS_ON_NODE=1
fi
source /etc/profile.d/modules.sh
-module load subread/1.5.0-intel stringtie/1.1.2-intel
+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}
mkdir ${pair_id}_stringtie
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 970bd01..6a2ba71 100644
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -62,7 +62,7 @@ module load python/2.7.x-anaconda picard/2.10.3 samtools/1.6 bedtools/2.26.0 snp
for i in *.bam; do
if [[ ! -f ${i}.bai ]]
then
- samtools index --threads $SLURM_CPUS_ON_NODE $i
+ samtools index -@ $SLURM_CPUS_ON_NODE $i
fi
done
--
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