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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 12:20:03 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -72,8 +72,15 @@ 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.
Optional inputs : Gcodes.txt and Conspecific.txt *Optional inputs : Gcodes.txt and Conspecific.txt
Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence summary. Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence summary.
* 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:
| EE_uc_Me03 | Universal |
| EE_uc_Me04 | Universal |
| EE_uc_Me05 | Universal |
| EE_uc_Me06 | Universal |
| EE_uc_Me07 | Universal |
### Processing genomes ### Processing genomes