How to get OTU table with corresponding fasta sequence

Dear All,
Is it possible to create a file following information in QIIME2

Column1:Taxa
Coulum2 to n of samples: corresponding OTU count in all samples
Column n+1: Corresponding fasta sequence.

I tried with the following commands:

qiime metadata tabulate --m-input-file taxonomy.qza --m-input-file table.qza --m-input-file rep-seqs.qza --o-visualization taxonomy.qzv

But I got the fasta sequence for each feature but couldn’t derive OTU counts for my samples. Is there anyway to resolve this issue?

Hi @steffi,

Just to clarify a couple of things. Do you need all this to be in one table or can this be in separate files? As it is, all the information you want can readily be obtained in separate files in qiime2. If were to hack something to put it all together in one table, then that file is no longer something useable in qiime2 and it would just for your own sake. Is this what you want?

Also, by taxa do you mean assigned taxonomy at a certain level or ASVs?

Hi @Mehrbod_Estaki

I need it as a one table

Thats great. Is it possible to merge all together by manually. If it so, that will be great for my analysis

I need assigned taxonomy (Bacterial classification) along with OTU counts

In principle you should be able to use metadata tabulate with FeatureData[Sequence] and FeatureData[Taxonomy], which gets you column1 and column n+1.

But for the feature-table, you will need to use qiime tools export and biom convert to turn that data into a TSV (fortunately it should be features as rows and samples as columns once finished, so at least you won’t have to transpose). There should be a lot of topics on the forum using export and biom convert, so hopefully you won’t run into anything too tricky.

Once you have both the merged FeatureData and the manually extracted FeatureTable, you should be able to just smash them together in Excel or your favorite spreadsheet editor. Hope that helps!

2 Likes

@ebolyen

Thank you . Ill try to get the required file

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.