convert txt to biom for import to shiny-phyloseq

joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

http://joey711.github.io/phyloseq/

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convert txt to biom for import to shiny-phyloseq #711

Closed StefPN closed 7 years ago

StefPN commented 7 years ago

Hi, My pipeline outputs the OTU table as a .txt and I need help converting it in order to used it in shiny-phyloseq. How do I do this? I attach a small table as an example. Thanks a lot for the help! /Stef ALL.unoise.vsearch_short.txt

joey711 commented 7 years ago

Most usearch/vsearch tools are going to be able to output a biom-format file. I would start by looking for how to do that, as it is a more effectively maintained solution. The biom-format companion tools in python (or R) can also probably get you there.

I'm going to close this for now, but feel free to post more details, especially if you feel that converting to biom-format in your current pipeline, or from those tools, is not possible for some reason.

Cheers