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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-28 13:58:51 -05:00
parent 5a9ca29d5c
commit eb716944ab
1 changed files with 11 additions and 11 deletions
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QuickStart-EukPhylo.md

@ -50,14 +50,14 @@ EukPhylo part 1 runs CDS (genome) or assembled transcripts (transcriptome) throu
``` ```
python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o Output_Folder --genetic_code Universal -d Databases > log.txt python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o Output_Folder --genetic_code Universal -d Databases > log.txt
``` ```
Here add detail of each option possible: Code flags:
* -1 = start script * -1 = start/first script to run.
* -2 = end script * -2 = end/last script to run.
* --assembled_transcripts = Folder with Assembled transcripts in fasta format * --assembled_transcripts = path to folder with Assembled transcripts in fasta format.
* -o = path to output folder * -o = path to output folder.
* --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional * --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional
* -d = path to Databases folder * -d = path to Databases folder.
* log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages * log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages.
### Output: ### Output:
> ReadyToGo files = AA, NTD > ReadyToGo files = AA, NTD
@ -85,10 +85,10 @@ To add the XPC option, only available for transcriptomes, user need to add the -
``` ```
python wrapper.py -1 1 -2 5 --cds CDS -o Output_Folder --genetic_code Gcodes.txt -d Databases > log.txt python wrapper.py -1 1 -2 5 --cds CDS -o Output_Folder --genetic_code Gcodes.txt -d Databases > log.txt
``` ```
Here add detail of each options possible: Code flags:
* -1 = start script * -1 = start/first script to run.
* -2 = end script * -2 = end/last script to run.
* --cds = Folder with CDS files in fasta format * --cds = path to folder with CDS files in fasta format.
* -o = path to output folder * -o = path to output folder
* --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional * --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional
* -d = path to Databases folder * -d = path to Databases folder