From 61c0f80dcd918312eb9fe5e21c7be8acd2375e6d Mon Sep 17 00:00:00 2001 From: marromesc Date: Mon, 1 Jul 2019 12:55:42 +0200 Subject: [PATCH] Update README.md --- README.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4d4194a..2483188 100644 --- a/README.md +++ b/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. + +