diff --git a/bcbio/ngsalign/tophat.py b/bcbio/ngsalign/tophat.py
index <HASH>..<HASH> 100644
--- a/bcbio/ngsalign/tophat.py
+++ b/bcbio/ngsalign/tophat.py
@@ -29,7 +29,7 @@ def _set_quality_flag(options, config):
     qual_format = config["algorithm"].get("quality_format", None)
     if qual_format.lower() == "illumina":
         options["solexa1.3-quals"] = True
-    else:
+    elif qual_format.lower() == "solexa":
         options["solexa-quals"] = True
     return options
Set quality flag properly for Tophat alignment.