From b682d7f7b0a8275711c5a2d45a25478ef5d7363e Mon Sep 17 00:00:00 2001
From: Erika Villa <Erika.Villa@utsouthwestern.edu>
Date: Sat, 12 May 2018 18:00:05 -0500
Subject: [PATCH] fix hisat cmd for read pair options
---
alignment/rnaseqalign.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index dabe941..8feea1b 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -59,9 +59,9 @@ else
module load hisat2/2.1.0-intel
if [ -s difffile ]
then
- 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
+ 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
else
- 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
+ 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
fi
if [[ $umi==1 ]]
then
--
GitLab