Updated README.

Added CrossMap functionality.
Added mm9 and hg19 support.

README.md

@@ -48,6 +48,7 @@ Required arguments:
 	--bed Path to BED-file
 	--genome_fasta Path to genome in FASTA-format
 	--jaspar_db Path to motif-database in MEME-format
+	--organism STRING Source organism: [ hg19 | hg 38 or mm9 | mm10 ]
 
 
 Optional arguments:
@@ -86,9 +87,10 @@ Optional arguments:
 	--motif_similarity_thresh FLOAT threshold for motif similarity score (Default: 0.00001)
 
 	Creating GTF:
-	--organism [homo_sapiens | mus_musculus]
-	--tissues
-
+	--tissues STRING Filter for tissue/category activity categorys as in JSON config (Default: None)
+    --wd PATH current working directory for the script (default: ".")
+    --dir PATH directory for saved Ensembl / UCSC file (default: "./data/")
+    --out PATH directory for the output GTF (default: ".")
 All arguments can be set in the configuration files.
  ```