From ad8abcc4fcd48ac13b50ffca89abfea57b6ea665 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Tue, 4 May 2021 01:28:49 +0200
Subject: [PATCH] Add usage instructions to the README
---
README.org | 14 ++++++++++++++
generation.sh | 2 +-
2 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/README.org b/README.org
index 7a312c4..cd40a40 100644
--- a/README.org
+++ b/README.org
@@ -33,3 +33,17 @@ nix-shell
After running these commands, you will find yourself in a shell that contains all the needed dependencies.
** Usage
+
+An execution script that accepts 2 parameters is provided, the following command invokes it:
+
+#+begin_src shell
+./generation.sh <number of sequences> <number of reads>
+#+end_src
+
+- <number of sequences>: an integer that specifies the number of different sequences to generate
+- <number of reads>: an integer that specifies the number of reads to perform on each sequence
+
+The script will generate 2 files under the data directory:
+
+| HVR.fastq | Contains the original CDR3 sequence |
+| CuReSim-HVR.fastq | Contains CDR3 after the read simulation, with sequencing errors |
diff --git a/generation.sh b/generation.sh
index 63fd8d7..330d939 100755
--- a/generation.sh
+++ b/generation.sh
@@ -1,7 +1,7 @@
#!/bin/sh
usage() {
- echo "usage: generation.sh <number of sequences> <number_of_reads>"
+ echo "usage: generation.sh <number of sequences> <number of reads>"
exit 1
}