I am new to running bacterial analysis. I have been running 16s pipeline v1 using Greengenes database. I was unable to get species specific data (most of my outputs looked like this k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f___;g___;s____, for example). I was advised to switch to the MicrobiomeHelper QIIME2 pipeline, as it is uses the SILVA database.
However, I found I encountered the same limitations in the output. Furthermore, I noticed that the output for SILVA and Greengenes were completely different. Some of the absolute quantities of the bacteria had similar numeric values, but none of the Order or Family names overlapped between the two. It appeared almost as if I were using two separate data sets (I had checked that I was not doing this).
Could anyone suggest what I may have been doing incorrectly based on this information?