diff --git a/hisat2/2.0.5/Hisat2_align.pl b/hisat2/2.0.5/Hisat2_align.pl
index b62de05..f879154 100644
--- a/hisat2/2.0.5/Hisat2_align.pl
+++ b/hisat2/2.0.5/Hisat2_align.pl
@@ -5,7 +5,7 @@
 use Getopt::Long qw(:config no_ignore_case no_auto_abbrev pass_through);
 
 my (@file_query, $database_path, $user_database_path, $annotation_path, 
-$user_annotation_path, $file_names, $root_names, @file_query2, $lib_type, $file_type, $n_cores);
+$user_annotation_path, $file_names, $root_names, @file_query2, $file_type, $n_cores);
 
 
 GetOptions( "file_query=s"      => \@file_query,
@@ -16,7 +16,6 @@
             "user_annotation=s" => \$user_annotation_path,
 	          "file_names=s"      => \$file_names,
 	          "root_names=s"      => \$root_names,
-	          "lib_type=s"        => \$lib_type,
 	          "file_type=s"       => \$file_type,
             "n_cores=s"         => \$n_cores,
           );
@@ -71,13 +70,12 @@
 
     my $app  = "/usr/bin/hisat2";
     my $format = $file_type;
-    my $library = $lib_type;
 
     chomp(my $basename = `basename $query_file`);
     $basename =~ s/\.\S+$//;
 
     if ($format eq "PE") {
-    	my $align_command = "$app $HISAT_ARGS --rna-strandness $library -x $name -1 $query_file -2 $second_file -p $n_cores | samtools view -bS - > $query_file.bam";
+    	my $align_command = "$app $HISAT_ARGS -x $name -1 $query_file -2 $second_file -p $n_cores | samtools view -bS - > $query_file.bam";
     	report("Executing: $align_command\n");
     	system $align_command;
     	system "samtools sort $query_file.bam $basename.sorted";
@@ -86,7 +84,7 @@
     	system "rm -rf *bam";
         }
     elsif($format eq "SE"){
-    	my $align_command = "$app $HISAT_ARGS --rna-strandness $library -x $name -U $query_file -p $n_cores | samtools view -bS - > $query_file.bam";
+    	my $align_command = "$app $HISAT_ARGS -x $name -U $query_file -p $n_cores | samtools view -bS - > $query_file.bam";
     	report("Executing: $align_command\n");
     	system $align_command;
     	system "samtools sort $query_file.bam $basename.sorted";
@@ -101,4 +99,4 @@
 
 sub report {
     print STDERR "$_[0]\n";
-}
\ No newline at end of file
+}