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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 12:59:29 -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
<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.
* Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence summary.
* **Main inputs** : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the scripts.
* **Outputs** : ReadyToGo files (AA and NTD), taxon summary, and sequence summary.
* *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.
* _Example:_
@ -93,4 +93,9 @@ Role of each script
| EE_uc_Me04 | Metatranscriptome |
| EE_uc_Me05 | Metatranscriptome |
To process transcriptomes, run:
'python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o . --genetic_code Universal -d Databases > log.txt'
### Processing genomes