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…
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:
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:
...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!