Hi @Hanna! QIIME 2 does not currently support CSS/DESeq normalization methods that are present in QIIME 1. The core development team doesn't have a timeline for adding this support, but we would welcome the addition of these methods in a QIIME 2 plugin if you or someone else is interested in developing that functionality (see our plugin developer docs for details).
I wonder if 100%OTUs of the sequence variants do not need the normalization any more.
I think they'll still need normalization because samples could still have vastly different sequence counts, which is what needs to be normalized.
Right now you have a few options to choose from:
- Rarefy your table with
qiime feature-table rarefy. - If you are interested in differential abundance testing in QIIME 2, take a look at the
qiime compositionplugin, which implements ANCOM (it has its own normalization scheme). - Run CSS/DESeq in QIIME 1 (or R) and import your normalized .biom file into QIIME 2 (see the importing tutorial).