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borenstein-lab / burrito

A visualization tool for exploratory data analysis of metagenomic data
https://elbo-spice.gs.washington.edu/shiny/burrito/
GNU General Public License v3.0
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Burrito and ASVs - is it possible? #33

Open nchorna812 opened 1 year ago

nchorna812 commented 1 year ago

I am trying to upload ASVs OTUs and custom taxonomy - getting error "OTUs are in the OTU table but are not present in the PICRUSt 16S normalization table". Is Burrito working with ASVs?

cnoecker commented 1 year ago

Hi, to use ASVs, you need to generate a custom contribution table (also known as stratified metagenome abundances) and taxonomy using PICRUSt2, which you can then upload to BURRITO. See the PICRUSt2 documentation here: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.5.0)#generate-metagenome-predictions

nchorna812 commented 1 year ago

Thank you very much!!!

From: Cecilia Noecker @.> Sent: Saturday, December 10, 2022 5:55:04 PM To: borenstein-lab/burrito @.> Cc: CHORNA,NATALIYA @.>; Author @.> Subject: Re: [borenstein-lab/burrito] Burrito and ASVs - is it possible? (Issue #33)

Hi, to use ASVs, you need to generate a custom contribution table (also known as stratified metagenome abundances) and taxonomy using PICRUSt2, which you can then upload to BURRITO. See the PICRUSt2 documentation here: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.5.0)#generate-metagenome-predictionshttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fpicrust%2Fpicrust2%2Fwiki%2FPICRUSt2-Tutorial-(v2.5.0)%23generate-metagenome-predictions&data=05%7C01%7Cnataliya.chorna%40upr.edu%7C22bdd05c773d4a7d057b08dadaf9326c%7C0dfa5dc0036f461599e494af822f2b84%7C0%7C0%7C638063061068718617%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UliPdJhQj3IrroAAXcBSk7eGXuNfliD8q%2FTkimZod6c%3D&reserved=0

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