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Updated Set up (markdown)

rebeccagawron 2024-01-05 12:09:29 -05:00
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Set-up.md

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## Transcriptomes ## Transcriptomes
### What you need in Transcriptomes folder: ### What you need in Transcriptomes folder:
* A folder called “<font color="orange">AssembledTranscripts</font>” with your assembled transcript fasta files * A folder called “**AssembledTranscripts**” with your assembled transcript fasta files
* A folder called “Databases” with the three folders: * A folder called “**Databases**” with the three folders:
* db_BvsE (how we ID likely-bacterial sequences) * db_BvsE (how we ID likely-bacterial sequences)
* db_StopFreq (for stop codon assignment) * db_StopFreq (for stop codon assignment)
* db_OG (this must be current version of the hook) * db_OG (this must be current version of the hook)
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* Files needed: * Files needed:
* Hook *.dmnd file ([Current version Hook-6.6.dmnd](https://drive.google.com/open?id=1ywYLZXzcTERDFCysz5vPbI9u6WRxz5r0&usp=drive_copy)) * 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)) * 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 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 * *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! * 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 * *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 *not required for all PhyloToL runs
## Genomes ## Genomes
### What you need in Genomes folder: ### What you need in Genomes folder:
* A folder called “CDS” with your CDS files * A folder called “**CDS**” with your CDS files
* A folder called “Databases” with the three folders: * A folder called “**Databases**” with the three folders:
* db_BvsE (how we ID likely-bacterial sequences) * db_BvsE (how we ID likely-bacterial sequences)
* db_StopFreq (for stop codon assignment) * db_StopFreq (for stop codon assignment)
* db_OG (this must be current version of the hook) * db_OG (this must be current version of the hook)
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* Files needed: * Files needed:
* Hook *.dmnd file ([Current version Hook-6.6.dmnd](https://drive.google.com/open?id=1ywYLZXzcTERDFCysz5vPbI9u6WRxz5r0&usp=drive_copy)) * 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)) * 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 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 * *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! * NOTE that this step is only if you are running genomes that all need specific genetic codes!
*not required for all PhyloToL runs *not required for all PhyloToL runs