Hi,
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,
Best,
Francisco
Well the best way would be to start over and do everything in mothur 
Alternatively, you could just use make.shared (http://www.mothur.org/wiki/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,
Francisco
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.