Documentation updates

README.md

@@ -24,24 +24,27 @@ The following quick start briefly summarizes the necessary steps to use our pipe
 
 1. Install the necessary tools (Snakemake, samtools, and bedtools)
 
-2. Clone the Git repository: ``git clone https://git.embl.de/grp-zaugg/diffTF``
+2. Clone the Git repository: 
 
-3. To run the example analysis, simply perform the following steps::
-  * Change into the *example/input* directory within the Git repository
+    ``git clone https://git.embl.de/grp-zaugg/diffTF``
+
+3. To run the example analysis, simply perform the following steps:
+
+    * Change into the *example/input* directory within the Git repository
   
-      ``cd diffTF/example/input``
+        ``cd diffTF/example/input``
       
-  * Download the data via the download script
+    * Download the data via the download script
   
-       ``sh downloadAllData.sh``
+        ``sh downloadAllData.sh``
     
-  * To test if the setup is correct, start a dryrun via the first helper script
+    * To test if the setup is correct, start a dryrun via the first helper script
   
-      ``sh startAnalysisDryRun.sh``
+        ``sh startAnalysisDryRun.sh``
     
-  * Once the dryrun is successful, start the analysis via the second helper script
+    * Once the dryrun is successful, start the analysis via the second helper script
   
-      ``sh startAnalysis.sh``
+        ``sh startAnalysis.sh``
     
 4. Modify the example analysis to run your own analysis. See Section 3 and 4 in the [Documentation](https://git.embl.de/grp-zaugg/diffTF/blob/master/doc/Documentation.pdf) for further details if you run into troubles or questions.