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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-28 14:09:17 -05:00
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QuickStart-EukPhylo.md

@ -50,15 +50,16 @@ 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
``` ```
Code parameters:
| Parameter | Description| | Parameter | Description|
| ----------- |----------------- | | ----------- |----------------- |
| -1 | start/first script to run.| | -1 | Start/first script to run.|
| -2 | end/last script to run.| | -2 | End/last script to run.|
| --assembled_transcripts | path to 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