diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index dabe9418a1aa9867389b26fa1fcc883650e68928..8feea1b1b759c4083e1c9654169b631a9817cc46 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