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Updated PhyloToL Part 1: GF assignment (markdown)

Katzlab 2024-08-13 18:30:29 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -132,7 +132,7 @@ The parameter options are:
## Output
When you run PhyloToL part 1 on **transcriptomic data** it will generate a folder called "Output" in the same folder as your "Scripts" folder. This Output folder will have the following structure:
When you run PhyloToL part 1 on **transcriptomic data** it will generate a folder called "Output" in the same folder as your "Scripts" folder. This Output folder should have the following structure (if it doesn't, something likely went wrong):
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL_trans_output_1.png" width="30%">
@ -140,7 +140,7 @@ The "ReadyToGo" folder contains the final cleaned output of PhyloToL part 1. The
PhyloToL part 1 also provides all intermediate files used in producing the above finalized outputs. Of greatest interest to most users here are likely to be the files in the `Intermediate/TranslatedTranscriptomes` folder, in which all intermediate files for each taxon are stored. Most importantly, users can find a record of all Diamond hits against the Hook Database (not filtered to keep only the best hits) in the file `DiamondOG/allOGresults.tsv`. This could be useful in trying to assess alternative gene family assignments. See the headers of each PhyloToL part 1 scripts for a description of the individual intermediate outputs.
The output of PhylToL part 1 when run on **genomic data** is very similar.
The output of PhylToL part 1 when run on **genomic data** is very similar, if a bit simpler. The key files (ReadyToGo and all Diamond hits against the Hook) are located in the same places, except there is no `TranslatedTranscriptomes` folder (key intermediate files are given directly in the `Intermediate` folder). Again, see the headers of each PhyloToL part 1 scripts for a more detailed description of the individual intermediate outputs.