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How to obtain a phylogenic tree #22

Closed CamillePhilippeSCI closed 1 week ago

CamillePhilippeSCI commented 1 month ago

Ask away!

Hello, I am willing to do Faiths phyolgeny test in R but in my outputs after EPI2ME 16s WF i have the taxonomic table and no phyloseq object. Could someone please tell me if it would be possible to create a phylogenic tree using this workflow ? Thankyou

nggvs commented 1 month ago

Hi @CamillePhilippeSCI , the wf doesn't create a phylogenic tree directly. You'd need to look into phyloseq input files/formats and write your own script for it Thank you very much for using the workflow!

CamillePhilippeSCI commented 1 month ago

Hi,

Thanks for your answer ! So you think that i can add lines in the WF to create it or do i have to start all over with a new script and the raw data ?

nggvs commented 1 month ago

Hi @CamillePhilippeSCI , If you want to add some lines to the wf, is fine, but then is going to be more difficult to update it (except if you feel comfortable using git). If not, I'd suggest to write a different script that reads the output directory (there is a copy of the abundance table there)