# Frequent Questions and "Best of the QIIME 2 Forum"
**URL:** https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608
**Category:** General Discussion
**Tags:** best-of-the-forum
**Created:** [February 13, 2020, 6:55pm UTC](https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608 "2020-02-13T18:55:53Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@q2d2](https://forum.qiime2.org/u/q2d2)
#### Post date: [February 13, 2020, 6:55pm UTC](https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608/1 "2020-02-13T18:55:53Z")
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. โถ
# FAQs
- [What is a "Feature" exactly? - #3 by Nicholas\_Bokulich](https://forum.qiime2.org/t/what-is-a-feature-exactly/2201/3)
- [MemoryError with q2-feature-classifier](https://forum.qiime2.org/t/feature-classifiers-error/11946/2)
- [How are ASV IDs generated?](https://forum.qiime2.org/t/how-are-asv-ids-generated/6075)
> **DADA2 Error Messages + FAQs (click to see titles)**
>
> - [Yes, primers must always be removed for DADA2 denoising](https://forum.qiime2.org/t/trimming-the-first-5-low-er-quality-bases-from-forward-and-reverse-reads-results-in-25-more-sequences-removed-as-chimeras/13768/5)
> - [Interpreting filtering stats: how many filtered reads is too many?](https://forum.qiime2.org/t/conceptual-justification-of-dada2-truncation-prior-to-merging/12882/16)
> - DADA2 fails to run due to 'Error in isBimeraDenovoTable'
> - [reads do not overlap following truncation](https://forum.qiime2.org/t/error-in-isbimeradenovotable-unqs-i-verbose-verbose-input-must-be-a-valid-sequence-table/11039/5)
> - [importing issues](https://forum.qiime2.org/t/dada2-fails-to-run-due-to-error-in-isbimeradenovotable/12344)
>
> - Error code 9: [this is a memory error](https://forum.qiime2.org/t/dada2-error-code-9/11867)
> - Mismatched forward and reverse sequence files
> - [Did pre-filtering remove some paired sequences?](https://forum.qiime2.org/t/error-with-dada2-script/13442)
> - [Do the files exist?](https://forum.qiime2.org/t/mismatched-forward-and-reverse-sequence-files-files-dont-exist/12511)
>
> - Error in table: attempt to make table with \>= 2^31 elements
> - [Sequence artifacts and low quality artificially inflate diversity](https://forum.qiime2.org/t/dada2-execution-halted-error-in-table-attempt-to-make-a-table-with-2-31-elements/11845)
>
> - โnamesโ attribute must be the same length as the vector
> - [really just another memory error encountered when multithreading](https://forum.qiime2.org/t/dada2-error-return-code-1/7140)
>
> - `incorrect number of subscripts on matrix`
> - dada2 is intended for marker-gene amplicon sequence data; shotgun sequence data [violates the assumptions of dada2](https://forum.qiime2.org/t/error-raised-during-denosing-step-with-dada2/4003/7), causing this error.
> - [all sequences are unique](https://forum.qiime2.org/t/denoising-paired-ends-with-dada2/8447/17) (e.g., as with shotgun sequences)
> - fake quality scores [cause dada2 to fail](https://forum.qiime2.org/t/doing-taxonomy-analysis-and-getting-abundancies-with-manifests/1202/19)
> **Importing and Demultiplexing FASTQ data (click to see titles)**
>
> - [Importing and Demultiplexing Sequence Data Quick Reference](https://forum.qiime2.org/t/importing-and-demultiplexing-sequence-data-quick-reference/14002)
> - [How to demultiplex without a barcode fastq?](https://forum.qiime2.org/t/demultiplexing/13255)
> **Various Taxonomy Classification Topics (click to see titles)**
>
> - [Unclassified/shallow classifications](https://forum.qiime2.org/t/train-you-classifier-taxonomy/3412/2)
> - [Custom databases, and more on unclassified sequences](https://forum.qiime2.org/t/custom-blast-database-fails-to-assign-taxonomy/12872/2)
> - [Confidence values](https://forum.qiime2.org/t/confidence-values-taxonomic-assignment/13199/2)
> - [Closed-reference OTU clustering vs. taxonomic classification](https://forum.qiime2.org/t/closed-reference-otu-picking-vs-taxonomic-annotation/13457/2)
> - [Taxonomic similarity vs. phylogenetic distance](https://forum.qiime2.org/t/does-it-make-sense-to-use-weighted-unifrac-distances-for-16s-data/12768)
> - [different results from self-trained full-length and v4 classifiers](https://forum.qiime2.org/t/different-results-from-self-trained-full-length-and-v4-classifiers/13604)
> **Understanding reference databases and taxonomy (click to see titles)**
>
> - [Greengenes Versus Silva](https://forum.qiime2.org/t/greengenes-versus-silva/13370)
> - [Greengenes Taxonomy: meaning of s\_\_; difference from \_\_](https://forum.qiime2.org/t/asv-collaps-question/11764/2)
> - [SILVA taxonomy: What does the "D" mean?](https://forum.qiime2.org/t/why-all-taxonomic-levels-on-barplot-have-d-letter/9239/4)
> - [Why does the same genus (Clostridium) appear in more than one family?](https://forum.qiime2.org/t/the-same-three-genus-belongs-to-different-family/13755)
> **interpreting PERMANOVA (click to see titles)**
>
> - [A visual illustration of how PERMANOVA works](https://forum.qiime2.org/t/beta-diversity-explanation-jaccard-distance/15216/11)
> - [P-values](https://forum.qiime2.org/t/understanding-beta-group-significance-permanova-results/12648/2)
> - [Interpretation](https://forum.qiime2.org/t/understanding-beta-group-significance-permanova-pairwise-statistics/10396)
> - [Sample sizes in beta-group-significance plots](https://forum.qiime2.org/t/unifrac-significant-group-over-inflating-ns/1043/3)
> - [Permanova vs. permdisp](https://forum.qiime2.org/t/adonis-betadiver-and-betadisp/9364)
- [Sample size calculation for microbiome studies](https://forum.qiime2.org/t/sample-size-calculation-for-microbiome-studies/12114)
> **Beta diversity and PCoA (click to see titles)**
>
> - [Emperor for... dummies?](https://forum.qiime2.org/t/emperor-for-dummies/13609)
> - [Emperor biplots: PCoA plots showing most important features](https://forum.qiime2.org/t/help-with-understanding-beta-diversity-calculation-results/17273/3)
> - [How to make 2D PCoA plots with ellipses](https://forum.qiime2.org/t/pcoa-plots-with-confidence-ellipsoids/11612)
> - [PCA vs. PCoA](https://forum.qiime2.org/t/pca-vs-pcoa-which-is-the-appropriate-one-for-microbiome-data/5974)
> - [Core metrics + what's going on under the hood](https://forum.qiime2.org/t/mistake-in-metadata-file-and-re-running-core-metrics-analysis/9979/2)
> - [Normalization for microbiome analysis](https://forum.qiime2.org/t/normalization-for-microbiome-16s-sequence-analysis/10398)
> - [Does it make sense to use weighted UniFrac for 16S data?](https://forum.qiime2.org/t/does-it-make-sense-to-use-weighted-unifrac-distances-for-16s-data/12768/5)
> - [Why are some weighted UniFrac distances greater than one?](https://forum.qiime2.org/t/why-some-of-the-weighted-unifrac-distances-are-lager-than-one/13636/4)
> **Interpreting ANCOM (click to see titles)**
>
> - [Interpreting W score](https://forum.qiime2.org/t/specify-w-cutoff-for-anacom/1844/10)
- [Parallelization: njobs vs. threads](https://forum.qiime2.org/t/threads-vs-nodes/11323)
- [Why do my quality score plots look so weird?](https://forum.qiime2.org/t/odd-display-of-demux-plot/13113/3)
- [Filter sequences based on length](https://forum.qiime2.org/t/filtering-out-asvs-from-dada2-based-on-length/9217/4)
- [Relabel feature table to use sequences as feature IDs](https://forum.qiime2.org/t/formatting-a-qiime2-feature-table-for-the-r-version-of-dada2/13387/4)
- [Yes it is okay to use forward reads only!](https://forum.qiime2.org/t/technical-support-re-illumina-want-to-use-only-forward-reads/9061)
- [OTUs vs. ASVs (QIIME 1 vs. 2): alpha diversity and other differences](https://forum.qiime2.org/t/esv-vs-otu-deflation-qiime1-vs-2/14867)
๐ ๐ ๐ฅ [Super helpful list of all alpha and beta diversity metrics](https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282) ๐ ๐ ๐ฅ
> **Where/how to publicly deposit sequence data? (click to see titles)**
>
> - [What is the correct way to submit amplicon sequencing data to NCBI](https://forum.qiime2.org/t/what-is-the-correct-way-to-submit-amplicon-sequencing-data-to-ncbi/11192)
> - [SRA submission process](https://forum.qiime2.org/t/generating-a-mapping-file/12179/4)
> **Longitudinal Analysis**
>
> - [How to do a paired tests on distance matrices](https://forum.qiime2.org/t/how-to-do-a-paired-tests-on-distance-matrices/12190)
> - [PCoA - Longitudinal study](https://forum.qiime2.org/t/pcoa-longitudinal-study/4185)
> - [Longitudinal analyses: LME vs Pairwise comparisons](https://forum.qiime2.org/t/longitudinal-analyses-lme-vs-pairwise-comparisons/13880)
> - [Singular matrix error - LME](https://forum.qiime2.org/t/singular-matrix-error-lme/13848)
# "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.
๐ These are tagged with the [best-of-the-forum tag](https://forum.qiime2.org/tag/best-of-the-forum)! ๐
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### Author:  [@Francisco](https://forum.qiime2.org/u/Francisco)
#### Post date: [February 20, 2020, 6:02am UTC](https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608/2 "2020-02-20T06:02:47Z")
DADA2 is not the only way to merge and clean sequences, i think this should be here:
> [@DADA2 vs Deblur](https://forum.qiime2.org/t/dada2-vs-deblur/2439/2):
>
> Hi @hulfred, I don't believe an independent benchmark has been performed yet to help inform a decision here. The algorithms do have similarities, and key differences. And to be transparent, I am a developer with Deblur. At a high level, DADA2 uses PHRED scores to inform an error model. Deblur deviates from this and instead uses a static error model. As a result, DADA2 is potentially better able to accommodate run specific errors. The benefit of a static error model though is that it potentiallโฆ
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 27, 2020, 10:44pm UTC](https://forum.qiime2.org/t/frequent-questions-and-best-of-the-qiime-2-forum/13608/5 "2020-02-27T22:44:50Z")