Qiime taxa collapse, what taxonomy.qza should be used?


(Xiaofan Wang) #1

I am new here, and trying to run the piecrust analysis in Galaxy. Before that I need to generate a OTU table that contains OTU ID, so I guess I need use qiime taxa collapse command. But how to generate taxonomy.qza? Which taxonomy file should I use? 99_otu_taxonomy.qza? 99_otus_v4.qza? Or taxonomy.qza? Thanks.


(Evan Bolyen) #2

Hey @Xiaofan_Wang,

Try using vsearch cluster-features-closed-reference instead (there’s a tutorial in the Community Tutorials section of this forum). That way all of your features will match the PICRUSt OTU IDs.