diff --git a/README.md b/README.md
index 131b443..a884632 100644
--- a/README.md
+++ b/README.md
@@ -89,13 +89,13 @@ Optional arguments:
 	--tomtom_treshold float	Threshold for similarity score. (Default: 0.01)
 
 	Motif clustering:
-  --cluster_motif BOOLEAN IF its 1 motifs will be clustered (Default: 0)
+  	--cluster_motif BOOLEAN IF its 1 motifs will be clustered (Default: 0)
 	--edge_weight INT Minimum weight of edges in motif-cluster-graph (Default: 5)
-  --motif_similarity_thresh FLOAT threshold for motif similarity score (Default: 0.00001)
+  	--motif_similarity_thresh FLOAT threshold for motif similarity score (Default: 0.00001)
 
-  Creating GTF:
-  --tissue STRING Filter for one or more tissue/category activity, categories as in JSON config (Default: None)
-  --organism STRING Source organism: [ hg19 | hg38 or mm9 | mm10 ] (Default: hg38)
+  	Creating GTF:
+ 	--tissue STRING Filter for one or more tissue/category activity, categories as in JSON config (Default: None)
+  	--organism STRING Source organism: [ hg19 | hg38 or mm9 | mm10 ] (Default: hg38)
 
 All arguments can be set in the configuration files.
  ```
diff --git a/bin/compareBed.sh b/bin/compareBed.sh
index 97e4a82..db58a2c 100644
--- a/bin/compareBed.sh
+++ b/bin/compareBed.sh
@@ -226,7 +226,7 @@ Rscript --vanilla $path/maxScore.R "$workdir"/pass1Fa.bed
 #echo "also get subsequences with no overlap of overlapping sequences"
 help=true
 
-if [ -d $"motifs" ]
+if [ -d "$motifs" ]
 then
 for i in "$motifs"/*.bed
 do