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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-24 16:34:37 -05:00
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QuickStart-EukPhylo.md

@ -71,12 +71,12 @@ To add the XPC option, only available for transcriptomes, user need to add the -
## Genomes:
### Set Up:
* A folder called “CDS” with your CDS 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
* * * Hook *.dmnd file ([Current version Hook-6.6.dmnd])
* * * Hook *.fasta file ([Current version Hook-6.6.fasta])
* A folder called “Databases” with the three sub folders:
* db_BvsE (how we ID likely-bacterial sequences)
* db_StopFreq (for stop codon assignment)
* db_OG
* Hook *.dmnd file ([Current version Hook-6.6.dmnd])
* Hook *.fasta file ([Current version Hook-6.6.fasta])
* A folder called “Scripts” filled with the 10 scripts from [here](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts) on Github. To run locally, pull out all scripts into main folder
### Running: