From .biom to SparCC analysis


I have an Otu_table.biom from QIIME and I want to run SparCC analysis at mothur.
What would be a feasible way to generate the requested “shared” file from my .biom table?

Thank you,

Well the best way would be to start over and do everything in mothur :slight_smile:

Alternatively, you could just use make.shared (

Hi I tried that before but I get the following error. It seems that it is not recognizing the .biom file.

mothur > make.shared(biom=otutable.biom)
Unable to open otutable.biom
No valid current files. You must provide a list or biom file before you can use the make.shared command.
[ERROR]: did not complete make.shared.

Thanks again,

That typically means that mothur can’t see the file otutable.biom because you or it are in the wrong folder. You might run system(ls) [mac/linux] or system(dir) [windows] and see if you can see otutable.biom.