Update README.md

README.md

@@ -6,52 +6,45 @@ CLONED using SOURCETREE from: https://bitbucket.org/young_computation/rose/src/m
 
 
 #### === Changelog
-1) USAGE
+1. USAGE
 
-- Option 1: To run the program locally and independent of software location by calling ROSE-local.sh
-	NB: First open ROSE-local.sh and modify PATHTO with the PATH ROSE is installed in.
-	> ROSE-local.sh ["GTF file"] ["BAM file"] ["OutputDir"] ["feature type"] ["species"] ["bed fileA"] ["bed fileB"]
+	- Option 1: To run the program locally and independent of software location by calling ROSE-local.sh
+		NB: First open ROSE-local.sh and modify PATHTO with the PATH ROSE is installed in.
+		> ROSE-local.sh ["GTF file"] ["BAM file"] ["OutputDir"] ["feature type"] ["species"] ["bed fileA"] ["bed fileB"]
 
-- Option 2: Add ROSE to user executable $PATH
-	```bash
-	PATHTO=/path/to/ROSE
-	PYTHONPATH=$PATHTO/lib
-	export PYTHONPATH
-	export PATH=$PATH:$PATHTO/bin
-	```
-
-1) Update: 
-
-* ROSE is executable independent of software directory location.
-* ROSE has a wrapper script "ROSE-local.sh" to successfully execute all steps of the package, else add ROSE to user executable $PATH
-* ROSE is compatible with python3
-
-1) DIRECTORY structure
-
-    ├── LICENSE.txt
+	- Option 2: Add ROSE to user executable $PATH
+		```bash
+		PATHTO=/path/to/ROSE
+		PYTHONPATH=$PATHTO/lib
+		export PYTHONPATH
+		export PATH=$PATH:$PATHTO/bin
+		```
 
-    ├── README.md
+1. Update: 
 
-    ├── ROSE-local.sh    : bash wrapper
+	* ROSE is executable independent of software directory location.
+	* ROSE has a wrapper script "ROSE-local.sh" to successfully execute all steps of the package, else add ROSE to user executable $PATH
+	* ROSE is compatible with python3
 
-    ├── lib
-
-        └── ROSE_utils.py   : utilities method
-    │   
-
-    └── bin
-
-        ├── ROSE_bamToGFF.py    : calculates density of .bam reads in .gff regions
-
-        ├── ROSE_callSuper.R    : ranks regions by their densities, creates cutoff
-
-        ├── ROSE_geneMapper.py  : assigns stitched enhancers to genes
-
-        └── ROSE_main.py    : main program
-
-    Total: 2 directories, 8 files
-
-1) DEPENDENCIES
+1. DIRECTORY structure
+	```bash
+	├── LICENSE.txt
+	│
+	├── README.md
+	│
+	├── ROSE-local.sh : bash wrapper
+	│
+	├── bin
+	│   ├── ROSE_bamToGFF.py : calculates density of .bam reads in .gff regions
+	│   ├── ROSE_callSuper.R : ranks regions by their densities, creates cutoff
+	│   ├── ROSE_geneMapper.py : assigns stitched enhancers to genes
+	│   └── ROSE_main.py : main program
+	└── lib
+	    └── ROSE_utils.py : utilities method
+
+	Total: 2 directories, 8 files
+	```
+1. DEPENDENCIES
 
 	* samtools
 	* R version > 3.4