Analysis microbial diversity

General Discussion
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1

Hello Qiime2 Community! I’m beginner in qiime2.

So, I have a question: I did my 16S rRNA sequencing using a kind of primier to bacteria and archaea. In this situation I did the qiime analysis using DADA2 and taken a table.tsv with all ASV to bacteria and archaea. But now, I want to analyze separately these two groups. There one way to separe this information in the DADA2 process? Or past the end analysis?

Thanks,

Jessy

2

Hi @jessybbio,

It sounds like your data is currently in R. If you’d like, you can bring it into QIIME 2 using the importing tutorial; then, you may want to filter your table by taxonomy. (There’s a nice tutorial for that). Although it may make a slight difference, my recommendation is to build your tree once. You can do that in QIIME 2 or some other program and import it.

Best,
Justine

1 Like
3

Hello @jwdebelius,

thanks for answer. You are right. My data is in R (table.tsv). I used in R script a function to separe bacteria and show only archaea and vice versa, but it doesent work to archaea. So I can’t show the cummulation curve and unifrac to archaea, because my tree file was did to two groups. But, is it possible to do a tree from archaea ASVs in the table.tsv and analize out of qiime environment? There any tutorial for that? Sorry if I didin’t got your explanation…

Thanks
Jessy

4

Hi @jessybbio,

We're the :qiime2: forum, and we primarily provide support for qiime 2. So, I can help walk you through how to get your data into qiime, filter your table, and then export it back to R; I can move this question over to a different section of the forum that addresses other tools; and/or you might find more R-specific help from the phyloseq or mothur groups, since both of those are based on R.

Best,
Justine

1 Like
5

Hi @jwdebelius,

In this case, could you explain me how to filter my table.qza?

Thanks,

Jessy

6

Hi @jessybbio,

You need to import your data into qiime using the importing data tutorial to get the table and taxonomy. You may need to convert from text to biom.

You can choose whether you also want to import your sequences; (my recommendation is to do so, but up to you). Then, you want to use the taxonomy filtering tutorial I linked above to make a table with only Bacteria (try --p-include Bacteria) .

Best,
Justine