diff --git a/Snakefile b/Snakefile
index dcde78388c68686da6d85ed924b01fbf554e4e7a..4b8811b50c9331db5ea7d165b6b71af6f706b14a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -286,7 +286,7 @@ rule prepare_strandphaser_config_per_chrom:
             print("compareSingleCells = TRUE",     file = f)
             print("callBreaks       = FALSE",    file = f)
             print("exportVCF        = '", config["sample"], ".txt'", sep = "", file = f)
-            print("bsGenome         = '", config["R_reference"], "'", file = f)
+            print("bsGenome         = '", config["R_reference"], "'", sep = "", file = f)