From 6ccac86107fce514c905ecffb1eee6fb846a0ea2 Mon Sep 17 00:00:00 2001
From: "Thulani Hewavithana (qnm481)" <qnm481@mail.usask.ca>
Date: Fri, 18 Aug 2023 17:52:41 -0600
Subject: [PATCH] Update README.md
---
README.md | 35 +++++++++++++++++------------------
1 file changed, 17 insertions(+), 18 deletions(-)
diff --git a/README.md b/README.md
index d4a9664..7839f52 100644
--- a/README.md
+++ b/README.md
@@ -291,20 +291,27 @@ of small blocks, small synteny blocks are incorporated into the
corresponding super-synteny blocks, taking into account the subgenome
placement of the super-synteny blocks as a reference.
-\- Usage No read in files Three input parameters: ws1, ws2 and ws3.
-
-Note: You need to select the most suitable window size parameters for
-subgenome1, subgenome2 and subgenome3.
+\- Usage No read in files or parameters.
\- Output The execution of SyntenyLink\_sb outputs number of output
-files: abc\_synteny\_chromosome\_names.success.colinear.xlsx,
-subgenome\_placement\_blocks.all.xlsx and
-subgenome\_placement\_blocks.all\_sub{k}.xlsx; There will be m number of
-files. k represents the corresponding subgenome number.
+files: modified\_chr\_names{k+1}.xlsx, subgenome\_placement\_blocks.all{k+1}.xlsx, subgenome\_placement\_blocks.all.xlsx. k represents the corresponding subgenome number.
-The abc\_synteny\_chromosome\_names.success.colinear.xlsx file holds the
+The modified\_chr\_names{k+1}.xlsx file holds the
replaced gene id\'s with there corresponding chromosome names which they
-bellong to:
+bellong to if they are not already placed inside the subgenome columns (to detect the genes that has been removed based on density threshold):
+
+Gene_id N1 N1.r N2 N2.r N3 N3.r N4 N4.r N5 N5.r N6 N6.r N7 N7.r
+AT1G01900 0 0 0 0 0 0 0 0 0 1 0 0 0 0
+AT1G01910 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+AT1G01920 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+AT1G01930 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+AT1G01940 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+AT1G01950 0 0 0 0 0 0 0 0 0 0 N6 0 0 0
+AT1G01960 0 0 0 0 0 0 0 0 0 0 0 1 0 0
+AT1G01970 0 0 0 0 0 0 0 0 0 1 0 0 0 0
+
+The subgenome\_placement\_blocks.all{k+1}.xlsx file holds the placement
+of genes in subgenomes optimal for each subgenome considering the subgenome separation optimal for each subgenome in step 4:
Row start # Row end # subgenome1 subgenome2 subgenome3
0 123 N10.r N9 N8.r
@@ -319,12 +326,6 @@ of genes in subgenomes in step 5:
124 698 N10 N8.r N9.r
699 1029 N6 N9.r N8.r
-The subgenome\_placement\_blocks.all\_sub{k}.xlsx file holds the optimal placement of genes in subgenomes for each subgenome. Ex: subgenome\_placement\_blocks.all\_sub1.xlsx::
-
-: Row start \# Row end \# subgenome1 subgenome2 subgenome3 0 75 N10.r
- N9 N8.r 76 78 N10.r N9.r N8.r 79 123 N10.r N9 N8.r 124 698 N10 N9.r
- N8.r
-
SyntenyLink\_mn
---------------
@@ -414,5 +415,3 @@ placemnet accuracy of each subgenome:
Exact match number for subgenome3: 5635
Missing genes for subgenome3: 2995
-Example
-=======
--
GitLab