YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-28 03:50:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Destroyed Set up (markdown)

Katzlab 2024-08-09 15:08:44 -04:00
parent 7587517213
commit 43759b64ca
1 changed files with 0 additions and 34 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

34
Set-up.md

@ -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