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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 16:16:04 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -92,7 +92,7 @@ Available parameters are:
| --maxlen |int|-| Maximum transcript length | | --maxlen |int|-| Maximum transcript length |
| --seq_count |int|-| minimum number of sequences after assigning OGs | | --seq_count |int|-| minimum number of sequences after assigning OGs |
#### To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run: #### To run the PhyloToL part 1 for both processing transcriptomes and removing sequences that resulted from index switching (cross plate contamination), run (LAk and ACL):
`python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt` `python Scripts/wrapper.py --first_script 1 --last_script 7 --assembled_transcripts AssembledTranscripts --output . --genetic_code Gcode.txt --databases Databases --xplate_contam --conspecific_names Conspecific.txt > log.txt`