From 86754e89879bb67b18206728a985208b6ea1630e Mon Sep 17 00:00:00 2001
From: rebeccagawron <122105684+rebeccagawron@users.noreply.github.com>
Date: Fri, 5 Jan 2024 11:26:58 -0500
Subject: [PATCH] Updated Set up (markdown)

---
 Set-up.md | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/Set-up.md b/Set-up.md
index 042e1d0..d1a032b 100644
--- a/Set-up.md
+++ b/Set-up.md
@@ -1,5 +1,4 @@
 ## Transcriptomes
-* Assembled transcripts
 ### What you need in Transcriptomes folder:
 * A folder called “AssembledTranscripts” with your assembled transcript fasta files
 * A folder called “Databases” with the three folders:
@@ -15,4 +14,21 @@
   * NOTE that this step is only if you are running transcriptomes that all need specific genetic codes!
 * *A file called “Conspecific.txt” filled with your 10-digit codes in a column tab separated with the conspecific (e.g. genus, species or metatranscriptome) names for each sample
 
+*not required for all PhyloToL runs
+
+## Genomes
+### What you need in Genomes folder:
+* A folder called “CDS” with your CDS files
+* A folder called “Databases” with the three folders:
+  * db_BvsE (how we ID likely-bacterial sequences)
+  * db_StopFreq (for stop codon assignment)
+  * db_OG (this must be current version of the hook)
+    * Current version is Hook-6.6 (08/04/23)
+    * Files needed:
+      * Hook *.dmnd file ([Current version Hook-6.6.dmnd](https://drive.google.com/open?id=1ywYLZXzcTERDFCysz5vPbI9u6WRxz5r0&usp=drive_copy))
+      * Hook *.fasta file ([Current version Hook-6.6.fasta](https://drive.google.com/open?id=1AN4_SmZUYFH6_xh2qOhyNUlFZ_NT9_-D&usp=drive_copy))
+* A folder called “Scripts” filled with the 10 scripts from [here on Github](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts)
+* *A file called “Gcodes.txt” filled with your 10-digit codes in a column tab separated with the genetic code designation for each sample
+  * NOTE that this step is only if you are running genomes that all need specific genetic codes!
+
 *not required for all PhyloToL runs
\ No newline at end of file