The following is a list of frequently asked questions on the forum, with answers, to serve as a point of reference for forum users to quickly find answers, or for forum users and moderators to use as a reference when helping others.
Note: some of these listings are collapsed lists. If you see an arrow next to a title, click the title to expand the list of topic titles related to that subject. 
FAQs
DADA2 Error Messages + FAQs (click to see titles)
- Yes, primers must always be removed for DADA2 denoising
- Interpreting filtering stats: how many filtered reads is too many?
- DADA2 fails to run due to ‘Error in isBimeraDenovoTable’
- Error code 9: this is a memory error
- Mismatched forward and reverse sequence files
- Error in table: attempt to make table with >= 2^31 elements
- ‘names’ attribute must be the same length as the vector
-
incorrect number of subscripts on matrix- dada2 is intended for marker-gene amplicon sequence data; shotgun sequence data violates the assumptions of dada2, causing this error.
- all sequences are unique (e.g., as with shotgun sequences)
- fake quality scores cause dada2 to fail
Importing and Demultiplexing FASTQ data (click to see titles)
Various Taxonomy Classification Topics (click to see titles)
Understanding reference databases and taxonomy (click to see titles)
interpreting PERMANOVA (click to see titles)
Beta diversity and PCoA (click to see titles)
- Emperor for... dummies?
- Emperor biplots: PCoA plots showing most important features
- How to make 2D PCoA plots with ellipses
- PCA vs. PCoA
- Core metrics + what’s going on under the hood
- Normalization for microbiome analysis
- Does it make sense to use weighted UniFrac for 16S data?
- Why are some weighted UniFrac distances greater than one?
Interpreting ANCOM (click to see titles)
Super helpful list of all alpha and beta diversity metrics
Where/how to publicly deposit sequence data? (click to see titles)
Longitudinal Analysis
“Best of the QIIME 2 Forum”
These topics are discussions of general interest to forum users on diverse, popular topics. These are similar to the FAQs, in that they should be of broad and general interest, but these instead provide in-depth information on specific topics, and ideally bring in voices from many different forum users.
These are tagged with the best-of-the-forum tag!