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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
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Question about previous filtering of otu table #334

Closed gonzalofe closed 8 months ago

gonzalofe commented 1 year ago

Hello. I previously filtered my phyloseq object to retain OTUs with a prevalence higher than 15% and then ran picrust2 with the otu table exported from filtered phyloseq and sequence fasta file exported from the raw phyloseq . My question is: will this differ from having exported the sequences from my filtered phyloseq object? or is it the same?

R-Wright-1 commented 11 months ago

Hello, apologies for the slow response. Some of the initial files placing the OTUs may differ, but the eventual output shouldn't be different as the abundance of each of your OTUs will be taken into account, so if they aren't present in the table but are in the fasta file then I don't think that should be an issue.

gonzalofe commented 11 months ago

Thank you for the answer.

El vie, 8 dic 2023 a la(s) 22:14, Robyn Wright @.***) escribió:

Hello, apologies for the slow response. Some of the initial files placing the OTUs may differ, but the eventual output shouldn't be different as the abundance of each of your OTUs will be taken into account, so if they aren't present in the table but are in the fasta file then I don't think that should be an issue.

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R-Wright-1 commented 8 months ago

I'm just closing this issue as it seems that it's been addressed now. Please let me know if it needs to be reopened.