diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index a96eaf6d2118942d52598ae79445883361c4d1b1..4df8b08d2980c339e0d630696b959774b1118d53 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -197,7 +197,7 @@ if (spike == 'yes') {
     reference = Channel.fromPath ("/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6/hisat2")
   }
 }
-reference.subscribe { println "$it" }
+//reference.subscribe { println "$it" }
 
 /*
  * trimData: trims any adapter or non-host sequences from the data
@@ -249,8 +249,8 @@ process alignReads {
   script:
     """
     if [ "${endsManual_alignReads}" == 'pe' ]; then
-    hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome -1 ${fqs[0]} -2 ${fqs[1]} 1>${repRID}.align.out 2>${repRID}.align.err;
-    else hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome -U ${fqs[0]} 1>${repRID}.align.out 2>${repRID}.align.err;
+    hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome ${stranded_alignReads} -1 ${fqs[0]} -2 ${fqs[1]} 1>${repRID}.align.out 2>${repRID}.align.err;
+    else hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${reference}/genome ${stranded_alignReads} -U ${fqs[0]} 1>${repRID}.align.out 2>${repRID}.align.err;
     fi;
     samtools view -1 --threads `nproc` -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
     samtools sort -@ `nproc` -O BAM  -o ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index 43ca2392078171ec9a1f42f7f9a83d13d0f0383b..f669cfa5f157aac7ec658c6cf6174ed98ff467fc 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -54,9 +54,12 @@ def main():
     # Get strandedness metadata from 'Experiment Settings.csv'
     if (args.parameter == "stranded"):
         if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
-            stranded = "stranded"
+            if endsManual == "se":
+                stranded = "--rna-strandness F"
+            else:
+                stranded = "--rna-strandness FR"
         elif (metaFile.Has_Strand_Specific_Information.unique() == "no"):
-            stranded = "unstranded"
+            stranded = ""
         else:
             print("Stranded metadata not match expected options: " + metaFile.Has_Strand_Specific_Information.unique())
             exit(1)
@@ -85,4 +88,4 @@ def main():
         print(species)
 
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()