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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 12:41:32 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -73,17 +73,22 @@ Role of each script
* 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.
* Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence summary. * Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence 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:
| Taxa | Genetic code | | Taxa | Genetic code |
| ----------- | --------- | | ----------- | --------- |
| EE_uc_Me03 | Universal | | EE_uc_Me03 | Universal |
| EE_uc_Me04 | Universal | | Sr_ci_Arsp | Ciliate |
| EE_uc_Me05 | Universal | | Sr_ci_Cpol | Peritrich |
| EE_uc_Me06 | Universal | | Sr_ci_Bjap | Blepharisma |
| EE_uc_Me07 | Universal |
* *The Conspecific.txt is similar and is only needed for cross plate contamination removal.
| Taxa | plate |
| ----------- | --------- |
| EE_uc_Me03 | Metatranscriptome |
| EE_uc_Me04 | Metatranscriptome |
| EE_uc_Me05 | Metatranscriptome |
### Processing genomes ### Processing genomes