Help with tables and bar plots in Qiime2

[Marie (Bertucci)]

Hello,

I am running Qiime2 to analyse some 16S data.
When look to the barplot on Qiime Viewer I have some results plotted.
However when I look to the table and the taxonomy files used to make this plot the results are different (for example the taxa of the second most abundant ASV is different, as well as the abundance). To be able to view these files I am exporting them to the right format before opening them in Excel for example.

I don’t know if this is a problem of file export ? Or is there any parameters in the plotting that are taken into account ?
I am quite novice in the domain…

Thanks in advance

[jwdebelius (Justine Debelius)]

Hi @Marie,

Welcome to the forum!

Let me answer your question in two parts: first, the absloute basics and then second, the theory behind it. This will be a relatively link-heavy post, because the good news is some of your questions have already been answered!

To get the taxonomic tables, you can click on the "CSV" button under downloads and this will give you a table which should work in Excel. (If it doesn't, please let us know!)

Alternatively, if you want to collapse the table yourself, check out the tutorial:

Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)

Creating a TSV BIOM table The following is based on a post by @gregcaporaso. $ qiime tools export table.qza --output-dir ./ $ biom convert -i feature-table.biom -o feature-table.tsv --to-tsv $ biom head -i feature-table.tsv # Constructed from biom file #OTU ID L1S105 L1S140 L1S208 L1S257 L1S281 4b5eeb300368260019c1fbc7a3c718fc 2222.0 0.0 0.0 0.0 0.0 fe30ff0f71a38a39cf1717ec2be3a2fc 5.0 0.0 0.0 0.0 0.0 d29fe3c70564fc0f69f2c03e0d1e5561 0.0 0.0 0.0 0.0 0.0 868528ca947bc57b69ffdf83e6b73bae 0.0 227…

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Okay, but the bigger question is why there's a difference in relative abundance between the relative abundance of your ASV and your graph. And thee short answer is that, for a lot of reasons, multiple ASVs carry the same taxonomic label. This is because of a number of methodological limitations.
However, we also have the problem that if you plotted 3000 ASVs on a barplot, (a) you'd run out of colors the human eye could distinguish (Its typically a range of 8 - 16 shades in people who aren't colorblind) (b) lots of ASVs don't appear in all samples (I think the most prevalent ASV in the American Gut was in about 80% of samples last I checked) and (c) lots of ASVs have relatively low abundance on average. ...So, we collapse them to make a bar chart that's easy to visualize.

There are a couple more threads that might help:

How should different ASVs of the same species be interpreted?

Hi guys! I understand this is a common question and discussed numerous times on different forums as to why this phenomenon happens and how to solve it (ignore it), but it would be nice to hear from some of you researchers as to how you interpret them in your research? Data coming out from ASVs methods such as dada2 is common to have multiple ASVs classified to the same species, most likely dominant species in the microbiome. My question is, is it generally accepted to treat these ASVs as diff…

Multiple entries for the Same Taxa and How do I retrive the corresponding Fasta sequence for each taxa

You are classifying ASVs. Just because two different ASVs (or even OTUs) have different sequences does not mean that they belong to different taxa. Different strains of the same species can have slightly different 16S sequences; even the same strain can have multiple 16S copies with very slightly different sequences. In your example, you are showing genus-level classifications. These different ASVs are all classified to the same genus — they could be different species in that genus, or differen…

When to collapse (the data, not yourself)

Sweet plots @devonorourke! I would personally avoid clustering on the front or back end. If you do it at either end, do it on the front and risk losing important information... but let the model tell you that! It is certainly interesting to test whether you receive similar (or more?) predictive power with taxonomy-collapsed features compared to ASVs. But that variation could be important. I'd say it's troublesome if you suspect these are the exact same species and exact same individua…

...The question of when to collapse your data, when it filter, when it rarify it are all complicated and things we continue to talk about here! So, if you'v got any more questions or thoughts please share them with us!

Best,
Justine