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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 13:08:28 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -71,8 +71,8 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
Role of each script Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%"> <img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
* **Main inputs** : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the scripts. * **Main inputs** : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the [Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Transcriptomes/Scripts).
* **Outputs** : ReadyToGo files (AA and NTD), taxon summary, and sequence summary. * **Outputs** : ReadyToGo files (AA and NTD) and taxon summary.
* *Optional inputs : Gcodes.txt and Conspecific.txt * *Optional inputs : Gcodes.txt and Conspecific.txt
* *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates. * *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates.
* _Example:_ * _Example:_
@ -102,7 +102,7 @@ To process transcriptomes, run:
* --output = path to output folder * --output = path to output folder
* --genetic_code = specified genetic code, name of .txt file with Genetic codes * --genetic_code = specified genetic code, name of .txt file with Genetic codes
* -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
### Processing genomes ### Processing genomes