Thanks to the forum, I imported my data into qiime and now I need to download a reference file from the human oral microbiome database. I thought the latest (2019) is better but there are two files and I don’t know which to use. Thanks in advance
Either one should work. I’m not sure if starting at position 9 or 28 is better.
If you scroll down that page, you will see a download link for
Taxonomy File for QIIME. You will want to pick that one up too, then follow this tutorial: Training feature classifiers with q2-feature-classifier.
Before you try using a new database, have you processed your data using the version of Silva that comes with Qiime2? SILVA is a very well curated database and is a standard in the field of microbiology. I would start with SILVA to set a baseline, then see if HOMD could improve upon it.
thanks a lot, colin for the help.