diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index d68c360..bf6f2a6 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -115,13 +115,11 @@ To run this step, you will need to add the '--xplate_contam' flag to the command ## Processing genomes -Running PhyloToL Part 1 on genomes requires at least 3 items in your main directory: 1) A folder named Scripts and containing all **[Scripts](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/Scripts)** from PhyloToL part 1 github, 2) a folder containing your **[CDS](https://github.com/Katzlab/PhyloToL-6/tree/main/PTL1/Genomes/TestData)** (as described above), and 3) a folder containing the **Databases** with three subfolders(db_BvsE (how we ID likely-bacterial sequences), db_StopFreq (for stop codon assignment), and db_OG (The hook database as described above)). Default script starts with your **CDS** and produces **ReadyToGo files** (nucleotide and amino acid sequences) of each taxa, and **summary information** of the sequences processed for those taxa. - - -* To run the PhyloToL part 1 for processing genomes, run: - `python Scripts/wrapper.py --first_script 1 --last_script 5 --cds CDS --output . --genetic_code Gcode.txt --databases Databases > log.txt` +PhyloToL part 1 uses a different but similar set of scripts to process input genomic CDSs (as opposed to assembled transcripts). The setup here is the same as described above, and running PhyloToL part 1 on genomic CDSs is similar to as described above for transcriptomes, except there is no option to remove contamination as a result of index hopping and no need to identify genetic codes to use in translation (start/stop codon positions are already known), so the process is simpler. We recommend always running scripts 1 through 5 in a single run, as follows: + `python Scripts/wrapper.py --first_script 1 --last_script 5 --cds CDS --genetic_code Gcode.txt --databases Databases > log.txt` +The parameter options are: | Parameter | Type| Options| Description| | ----------- | ----------------- |----------- | ----------------- |