feature table with rep seqs and samples ID

Hi Qiime2 wizards!!

I'm tring to locate some sequences in my rep_seq file after dada2 and relate them with their corresponding sample ID...

Specifically, I'm analysing the effect of the addition of some strains in soil samples... thus, I want to locate the sequences from my strains in the samples. Analyzing the rep_seqqza file after dada2, I can see the sequences and the number of samples they can be found in. However, I cannot know what are those samples... and for me it is very important if they are located in treated soils or control ones... I already locate the sequences by downloading the fasta file... but I don't know what are the samples where they were detected.

Thank you in advance.

Ana =)

Hello Ana,

The answer to this question is in the core semantic types offered by Qiime2.

That is FeatureData[Sequence], which links sequence with feature ID.

You will also need FeatureTable[Frequency], which links feature ID and sample ID.
Then you will need sample metadata, which links sample IDs to their metadata context, like soil treatment group.

It goes like this:

feature sequence
:arrow_up_down: FeatureData[Sequence]
feature ID
:arrow_up_down: FeatureTable[Frequency]
sample ID
:arrows_clockwise: metadata
soil treatment groups for those samples

This question is tricky because it requires a mental model linking together the data structures of Qiime2. We should probably have a diagram that explains this :technologist: :framed_picture:

Great! and how can obtain this kind of results? I mean, I already have both FeatureTables (after dada2 you got rep. sequences and frequency table), and also the metadata table... but I don't know how to get the table I need... just a table similar to the Frequency Table but with all the samples and the number of times I got each sequence in each sample...

Sorry, I'm almost new in all the Qiime2 world...

Thank u in advance!!

Here is an example of FeatureTable[Frequency]

ASV:SampleID Sample1 Sample2 Sample3
asv1 123 456 789
asv2 25 69 22
asv3 111 22 3

Here is an example of FeatureData[Sequence]

ASV sequence

Because the ASV column is shared between these two tables, you can join them to get the table you described using R, Python, or Excel/Google Docs:

sequence ASV:SampleID Sample1 Sample2 Sample3
ATCCTG asv1 123 456 789
ATTTCG asv2 25 69 22
ATTGCC asv3 111 22 3

Are you asking about how to perform this join? What kinds of software do you have experience with?

Hi colin! my main problem is that I dont get the FeatureTable[Frequency]... I'm running dada2 with the following command:

time qiime dada2 denoise-single --i-demultiplexed-seqs 16S.qza --p-trunc-len 280 --output-dir dada2 --verbose

And afterwards I've 3 files: the stats, with the quality filter info, the rep.seqs file, with the following info:

Feature ID Sequence Length Sequence

and the table.qza, similar to this:

Frequency # of Samples Observed In
565510dc4fd6dc5637f352518bcad024 19,277 5
a29d551ec1784e2d4c623a6dc65a7ebb 15,773 5
ef7f45e97788eee3959ece505f84a23f 9,200 5

So I just have the number of samples observed in, but I don't know which samples are... So how can I get the FeatureTable[Frequency] with the sampleID and the samples... It would be amaizing get that!

Thank you in advance!

Ah ha!

Let's talk about that dada2 output table, using this section of the pd-mice tutorial as an example.

First, we run
qiime dada2 denoise-single ... --o-table ./dada2_table.qza,
and later we run
qiime feature-table summarize ... --o-visualization ./dada2_table.qzv

That is the output of feature-table summarize, which is a .qzv file.
Go back a step to the output of dada2 denoise-single, which is a .qza file. Export the contents of that file and open it up with a text editor. Inside there is the table we are looking for.

We are so close! Let me know what you find!

I tried with the following script:

qiime tools export --input-path table.qza --output-path exported-table

but it is a biom table... is it possible to export into a .txt or excel table?

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Ok got it!! thank you very much!!! I've been trying for days and finally I got it!! really thanks!

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