diff --git a/snakemake/paired_end.snakefile b/snakemake/paired_end.snakefile
index 23fb6e9e770ce720898fa641f392772ad09ce322..3488d27af05cf9e80aebe32c5b41715c498020de 100644
--- a/snakemake/paired_end.snakefile
+++ b/snakemake/paired_end.snakefile
@@ -335,7 +335,7 @@ rule pe_genome_quantification_kallisto:
 		-i {input.index} \
 		-o {params.output_dir} \
 		--pseudobam \
-		--{params.directionality}-stranded \
+		{params.directionality} \
 		{input.reads1} {input.reads2} > {output.pseudoalignment}) &> {log}"
 
 
diff --git a/snakemake/single_end.snakefile b/snakemake/single_end.snakefile
index 7c6b2acb6bae449942bf2056465a2392f5ac019d..5c06dac92f7e4fe35236b0bf3f7f853c312c1370 100644
--- a/snakemake/single_end.snakefile
+++ b/snakemake/single_end.snakefile
@@ -259,7 +259,7 @@ rule genome_quantification_kallisto:
 		-l {params.fraglen} \
 		-s {params.fragsd} \
 		--pseudobam \
-		--{params.directionality}-stranded \
+		{params.directionality} \
 		{input.reads} > {output.pseudoalignment}) &> {log}"
 
 		
\ No newline at end of file