From 43759b64ca53b13c82e6a81664c62e7f614de2e7 Mon Sep 17 00:00:00 2001 From: Katzlab Date: Fri, 9 Aug 2024 15:08:44 -0400 Subject: [PATCH] Destroyed Set up (markdown) --- Set-up.md | 34 ---------------------------------- 1 file changed, 34 deletions(-) delete mode 100644 Set-up.md diff --git a/Set-up.md b/Set-up.md deleted file mode 100644 index 3d29d34..0000000 --- a/Set-up.md +++ /dev/null @@ -1,34 +0,0 @@ -## Transcriptomes -### What you need in Transcriptomes folder: -* A folder called “**AssembledTranscripts**” with your assembled transcript fasta 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 14 scripts from [here on Github](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/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 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