Hi Eric Daliri -

If have a phyloseq object created in R then you can find the codes to convert your phyloseq object to lefse format output file in R using this script https://github.com/seashore001x/Rrumen/blob/master/phyloseq2lefse.R

The output can then be uploaded to galaxy server of lefse directly.

http://huttenhower.sph.harvard.edu/galaxy/

Best wishes,

Sudarshan

Hi Eric Daliri -

If have a phyloseq object created in R then you can find the codes to convert your phyloseq object to lefse format output file in R using this script https://github.com/seashore001x/Rrumen/blob/master/phyloseq2lefse.R

The output can then be uploaded to galaxy server of lefse directly.

http://huttenhower.sph.harvard.edu/galaxy/

Best wishes,

Sudarshan

Thanks you Sudarshan. I will try your suggestion

Hi Eric Daliri ,

Something to keep in mind when predicting function based on 16S rRNA sequence data is that you are only inferring function. In an ideal world, you would have some transcriptomic or proteomic data to back it up. A method that serves as a bit of a comprise is using a metagenomic approach that sequences and to a certain degree, allows you to quantify which members of the microbial community are present in addition to including functional gene sequences.

I have just recently jumped into the world of metagenomics but I have used these papers as a starting point (I have included an example that focuses on cases in the gut, and another one that focuses on biogeochemical gradients for your reference):

Article Best practices for analysing microbiomes

Article Critical biogeochemical functions in the subsurface are asso...

These papers highlight additional methods that you can consider.

I hope this helps,

Daniel

Thanks Gregoire