diff --git a/config/default.yml b/config/default.yml
index 7cc8e55..1ebada4 100644
--- a/config/default.yml
+++ b/config/default.yml
@@ -56,7 +56,7 @@ reference:
 #
 salmon:
   index_flags: '--gencode'
-  quant_flags: '--gcBias'
+  quant_flags: '-l ISR --gcBias'
 
 #
 # The HTStream section
diff --git a/src/salmon.snake b/src/salmon.snake
index 73b16ed..4b97be3 100644
--- a/src/salmon.snake
+++ b/src/salmon.snake
@@ -47,5 +47,5 @@ rule salmon_quant_se:
   version: SALMON_VERSION
   shell:
     """
-    salmon quant -p {threads} -i {input.index} -l ISR -r {input.r1} -o {config[dirs][quant]}/{wildcards.sample} {params.flags} &> {log}
+    salmon quant -p {threads} -i {input.index} -r {input.r1} -o {config[dirs][quant]}/{wildcards.sample} {params.flags} &> {log}
     """