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ravel-lab / VALENCIA

VAginaL community state typE Nearest CentroId clAssifier
MIT License
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qiime2 conversion script - DADA2 1.8 pipeline compatibility #3

Open MChapa1 opened 3 years ago

MChapa1 commented 3 years ago

Hello there, I would like to know if it is possible to use the ASV tables obtained through the DADA2 pipeline in R (https://benjjneb.github.io/dada2/tutorial_1_8.html) as input for the qiime2 conversion script. Thanks in advance.

JLammons14 commented 9 months ago

This may be too late, but I recently built a small R package that could help you out. It can convert a phyloseq object to the Valencia format and can run Valencia in R environments. So if you put the output of the DADA2 pipeline into a phyloseq object you should be able to easily convert it to the format Valencia needs. I've linked the related github page here: https://github.com/JLammons14/ValenciaInR

Sada-mwatelah commented 9 months ago

Thank you for this response. This is still helpful.

Kind regards, Ruth

From: Lemon_Head @.> Sent: Friday, September 22, 2023 1:47 PM To: ravel-lab/VALENCIA @.> Cc: Subscribed @.***> Subject: Re: [ravel-lab/VALENCIA] qiime2 conversion script - DADA2 1.8 pipeline compatibility (#3)

This may be too late, but I recently built a small R package that could help you out. It can convert a phyloseq object to the Valencia format and can run Valencia in R environments. So if you put the output of the DADA2 pipeline into a phyloseq object you should be able to easily convert it to the format Valencia needs. I've linked the related github page here: https://github.com/JLammons14/ValenciaInR

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