From 8a0d2f780987ae483f6b5640440f44045c64ff23 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 17 Oct 2024 15:01:17 +0300
Subject: Add new step for writing rqtl script in rqtl-2.

---
 topics/lmms/rqtl2/gn-rqtl-design-implementation.gmi | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/topics/lmms/rqtl2/gn-rqtl-design-implementation.gmi b/topics/lmms/rqtl2/gn-rqtl-design-implementation.gmi
index 2920247..ca30aef 100644
--- a/topics/lmms/rqtl2/gn-rqtl-design-implementation.gmi
+++ b/topics/lmms/rqtl2/gn-rqtl-design-implementation.gmi
@@ -43,11 +43,23 @@ We will address these challenges and add  enhancements by:
 
 
 ## High-Level Design
-This is divided into two major components:
-* RQTL Api
+This is divided into three major components:
 
+* GN3 RQTL-2 Script implementation
+* RQTL Api
 * Monitoring system for the rqtl script
 
+
+### GN3 RQTL-2 Script implementation
+We currently have an rqtl script written in rqtl https://github.com/genenetwork/genenetwork3/blob/main/scripts/rqtl_wrapper.R
+There is a newer rqtl implementation (rqtl-2) which is
+a ) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.
+To see the difference between the two:
+=> oWe aim to implement a seperate script using this while maintaining the  one
+eimplemented using rqtl1.
+(TODO) This probably needs to be split to a new issue(with enough knowledge) , to capture
+each computation step .
+
 ### RQTL Api
 
 
-- 
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