# some confusion about the feature table of qiime2
**URL:** https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665
**Category:** General Discussion
**Tags:** feature-table
**Created:** [February 18, 2020, 4:57am UTC](https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665 "2020-02-18T04:57:03Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Daryl](https://forum.qiime2.org/u/Daryl)
#### Post date: [February 18, 2020, 4:57am UTC](https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665/1 "2020-02-18T04:57:03Z")
I am a beginner in bioinformatics. As far as I know, there are three ways to generate feature table in qiime2:
1. dada2
2. delur
3)the method of dereplicate-sequences in q2-vesearch
I'm not sure whether the feature table generated by these three methods is the same thing. These three should be the same. If so, \*\*feature table is nothing but dereplicate-sequences？ \*\*
Some people said that feature table is different from OTUs and can be regarded as 100% OTUs. I know that OTU is the result of sequence clustering. **So 100% OTU means no clustering, just the sequence after dereplicated?**
**So,feature table is a sequence set after dereplicate, feature table will generate OTUs if further clustering is carried out. Is this correct?**
In addition, I found ASVs (example sequence variants) in some tutorials. Is this the alias of feature table?
Any answer to my question is appreciated.Thank you in advance.
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [February 18, 2020, 9:41am UTC](https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665/2 "2020-02-18T09:41:06Z")
Hi @Daryl,
Let's take a step back. A "feature table" is a tabular representation of your data where we map samples to some kind of feature (ASVs, OTUs, species, metabolites, genes, cytokines, cities visited, nutrients... if you can represent it as a feature table, you can represent it as a feature table!). In QIIME (and microbiome bioinformatics specifically), the feature table typically looks something like this under the hood:
| sample-id | 👩🌾 | 👩💻 | 🕵️♀️ |
| --- | --- | --- | --- |
| 🦀 | 5 | 0 | 500 |
| 🐔 | 100 | 200 | 50 |
| 🐖 | 0 | 5000 | 30 |
| 🥦 | 0 | 0 | 10 |
Due to legacy reasons, we typically represent the features (here 🦀, 🐔, 🐖, 🥦 ) as the rows and the samples (👩🌾, 👩💻, 🕵️♀️) are the columns. We can also represent the data as relative abundance, rather than counts. But... those are details.
> [@Daryl](#):
>
> As far as I know, there are three ways to generate feature table in qiime2:
>
> 1. dada2
> 2. delur
>
> 3)the method of dereplicate-sequences in q2-vesearch
>
> I’m not sure whether the feature table generated by these three methods is the same thing.
They _primary_ ways to generate a feature table in QIIME 2 from amplicon data dada2, deblur, and clustering via vsearch to make OTUs (I recommend the [tutorial here](https://docs.qiime2.org/2019.10/tutorials/otu-clustering/) for more details on OTU clustering.) Essentially, though, after you take the dereplicated sequences from vsearch, you then cluster those to generate a table like the one above.
You can learn more about all the different kinds of features here:
> [@What is a "Feature" exactly?](https://forum.qiime2.org/t/what-is-a-feature-exactly/2201):
>
> Hi I am doing the "Moving Pictures" tutorial, but I don't understand the "feature" meaning, and it seems to be a core concept in QIIME 2. Can you help me with that? Sorry if the question is too basic. Thank you
> [@Daryl](#):
>
> Some people said that feature table is different from OTUs and can be regarded as 100% OTUs. I know that OTU is the result of sequence clustering. **So 100% OTU means no clustering, just the sequence after dereplicated?**
A 100% OTU (also zOTU or sOTU [zeroOTU or subOTU]) is usually the same as an ESV (exact sequence variant) or ASV (amplicon sequence variant). This _should_ be the output of one of the denosing algorithm: dada2 or deblur. You want to denoise to get this output because denoising addresses error in your sequences. If you use the directly dereplicated sequences, you'll introduce error from PCR and sequencing.
The ASVs or raw sequences can then be clustered into operational taxonomic units (OTUs) which are just clusters of sequences with some threshold of similarity.
Here's a really nice discussion about OTUs and ASVs, etc
> [@To cluster or not to cluster?](https://forum.qiime2.org/t/to-cluster-or-not-to-cluster/10022):
>
> Hello - I would like to bring up a topic that has been discussed before ([https://forum.qiime2.org/t/a-quick-clarification-on-clustering/1237?u=shira](https://forum.qiime2.org/t/a-quick-clarification-on-clustering/1237)) and provide an example from my own analysis. I am looking at one particular taxonomic group within environmental samples of bacterial populations. The method of denoising is dada2, so I am assuming that OTU clustering was not necessary since sequencing errors are accounted for during the denoising process. However, this analysis resulted in many O…
ASVs and OTUs are one _kind_ of feature a table can contain. But if you used something like [q2-PICRUSt](https://library.qiime2.org/plugins/q2-picrust2/13/), your feature table might contain genes. If you use q2-taxa and collapsed your taxonomy, your feature table would contain the collapsed taxonomy. If you have metabolomics and you have [q2-metabolomics](https://library.qiime2.org/plugins/q2-metabolomics/10/) then your features are molecules. You could even make a feature table out of metagenomics data using [q2-metaphlan](https://library.qiime2.org/plugins/q2-metaphlan2/12/) or [q2-shogun](https://library.qiime2.org/plugins/q2-shogun/15/).
Best,
Justine
---
### Author:  [@Daryl](https://forum.qiime2.org/u/Daryl)
#### Post date: [February 24, 2020, 1:57pm UTC](https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665/4 "2020-02-24T13:57:53Z")
Oh，Jesus.It must be too late to reply now！But please accept my sincere thanks. I had read your wards about the feature table.Very clear,very logical~the discussion about whether clustering or not clustering is very interesting and useful.I had read through everyone's view on that issue. To my best knowledge，the sequences after dereplicated is should be ASVs.Of course,coures,the fiter and quality control is requisite.however,otherviews suggest that sequences must turn into ASVs after deduplicated and 100% clustered.it can compare the output of [dereplicate-sequences: Dereplicate sequences.](https://docs.qiime2.org/2019.10/plugins/available/vsearch/dereplicate-sequences/) and [cluster-features-de-novo: De novo clustering of features.](https://docs.qiime2.org/2019.10/plugins/available/vsearch/cluster-features-de-novo/).by the way, i found some sentence in the tutorial of OTU picking strategies in QIIME can may support my point that [If you’re interested only in dereplicating sequences as your OTU picking process, that is a special case of de novo clustering where the similarity threshold is 100%.]([OTU picking strategies in QIIME — Homepage](http://qiime.org/tutorials/otu_picking.html)
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [February 24, 2020, 2:46pm UTC](https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665/5 "2020-02-24T14:46:09Z")
Hi @Daryl,
The topic is still open so it's certainly not to late! You may want to look into this topic:
> [@Why shouldn't I just filter based on quality score and throw away those with low scores?](https://forum.qiime2.org/t/why-shouldnt-i-just-filter-based-on-quality-score-and-throw-away-those-with-low-scores/11452):
>
> Hi, Using dada2 or deblur is essentially taking out the low quality data. Is there a reason I should use one of these and not just filter based on the quality score? Thanks.
However, your dereplicated sequences dont account for PCR error, which denoising solves!
Best,
Justine
---
### Author:  [@Daryl](https://forum.qiime2.org/u/Daryl)
#### Post date: [February 24, 2020, 2:49pm UTC](https://forum.qiime2.org/t/some-confusion-about-the-feature-table-of-qiime2/13665/6 "2020-02-24T14:49:09Z")
ok~i will see that
best wishe 😁