make.biom in a batch

Theory behind mothur
1

Is there a way to add make.biom to a batch file? current wouldn’t work because I’d need to specify subsampled and a particular level?

2

You can run the make.biom file with just a shared file as input:

mothur > make.biom(shared=yourSharedFile)

or

mothur > make.biom(shared=current)

3

Thanks Sarah, but that wouldnt’ have the taxonomy info would it? That’s what people are wanting as part of a biom so they can use phyloseq/bioconductor. I’ll have to keep thinking on this.