diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index e9eee45e1e7030d43f6a01083459fa43a31da2d1..ddb3e6302b330cd035c9fff1593e29dcbbf85c77 100644
--- a/snakemake/Snakefile
+++ b/snakemake/Snakefile
@@ -156,16 +156,16 @@ rule generate_alfa_index:
 			-p {threads} \
 			-o {params.out_dir} &> {log}"
 
-rule star_rpm:
-	''' Create bedgraph coverage with STARs RPM normalisation '''
+rule star_rpm_stranded:
+	''' Create stranded bedgraph coverage with STARs RPM normalisation '''
 	input: 
         "/scicore/home/zavolan/burri0000/test_alfa/sample/chr21.bam"
 	output:
-		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
-		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+		"/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
 	params:
-		out_dir = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/",
-		filenameprefix = "/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_"
+		out_dir = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/",
+		filenameprefix = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_"
 	singularity:
 		"docker://zavolab/star:2.6.0a"
 	threads: 4
@@ -187,8 +187,8 @@ rule star_rpm:
 rule run_alfa_bg_stranded:
 	''' Run ALFA from stranded bedgraph files '''
 	input:
-		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
-		"/scicore/home/zavolan/burri0000/test_alfa/sample/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
+		str1 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str1.out.bg",
+		str2 = "/scicore/home/zavolan/burri0000/rnaseqpipeline/star_rpm/STAR_Signal.UniqueMultiple.str2.out.bg"
 	output:
 		directory("output/")
 	params: