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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-13 10:28:01 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -92,9 +92,20 @@ 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 (LAk and ACL):
####Index Switching (Cross plate contamination)
As you run PhyloToL part 1 on transcriptomes, you might want to remove sequences from your assembled transcripts that are a result of index switching. This is done by (LAK and ACL on XPC removal process with conspecific file). To include this parameter to your PhyloToL part 1 run, you will need to add the '--xplate_contam --conspecific_names Conspecific.txt' flag to the command line as follow:
`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`
Example of a Conspecific.txt file
| Taxa | plate |
| —------------ | —------------------ |
| EE_uc_Me04 | Metatranscriptome |
| EE_uc_Me05 | Metatranscriptome |
| EE_uc_Me06 | Metatranscriptome |
| EE_uc_Me07 | Metatranscriptome |
### Processing genomes ### Processing genomes