Update README.md

README.md

@@ -4,4 +4,17 @@ This is my Master Thesis project.
 
 ## miRPIPE program
 
-In this miRPIPE directory there are scripts that you can run to reanalyze the data. Also feel free to use with your own data. 
+In this miRPIPE directory there are scripts that you can run to reanalyze the data. Also feel free to use with your own data.
+
+The scripts create a working directory and batch files that you have to run if you want to analyze the samples.
+
+To install the scripts you can run one by one:
+*chmod +x script_name.sh*
+
+### batch_prepro_bench.sh
+
+**Usage:** *batch_prepro_bench.sh /home/user/working_directory /path/to/SraRunTable.txt samples_downloaded adapter_ask adapter_sequence*
+If adapter_ask is 0, it means that there is no adapter. Type 1 in adapter_ask to guess the adapter or 2 if there is an adapter.
+If you have already downloaded the samples type 1 in samples_downloaded.
+
+