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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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KEGG analysis from phyloseq object #1082

Open owenNewcastle opened 5 years ago

owenNewcastle commented 5 years ago

I'm investigating biofilms living on plastic debris. I want to find out if there is differential expression of certain KEGG Orthologs (KO) at week 0 and week 7 of my microcosm experiment (as well as between different treatments - all of which are variables in my phyloseq object.

Can someone help by directing me towards a software and output file (from my phyloseq object) in which I could do KEGG analysis?

For example I looked into PICRUSt, although this requires a .biom which can only work with OTUa that were picked by closed reference OTU picking. I processed my raw reads with dada2 and therefore there is debate over what to call the output from this (see: https://github.com/benjjneb/dada2/issues/62). Is KEGG analysis downstream from dada2/phyloseq outputs/figures?

If this would be more appropriate to post on the dada2 page just let me know an I will move it.

MSMortensen commented 5 years ago

Hi,

This is not the right place to ask for dada2 to PICRUSt workflows, but if you haven't found it already I suggest you skip directly to PICRUSt2 as it is made to work with ASV.

https://github.com/picrust/picrust2/wiki

Enjoy!