Finding the list of sequences that belong to a given OTU after clustering (apart from the representative sequence)

[Maryam (Maryam Elfeki)]

Hi all,

So I am clustering functional genes (not 16S) and I am trying to figure out which clustering percentage yields groups of sequences (let’s call them OTUs, for short) with the same function.

I followed the “moving tutorial” process, I used DADA2 for quality control and then I proceeded with clustering using the vsearch de-novo clustering method .The command I used for this is:

qiime vsearch cluster-features-de-novo
–i-table table.qza
–i-sequences rep-seqs.qza
–p-perc-identity 0.80
–o-clustered-table table-dn-80.qza
–o-clustered-sequences rep-seqs-dn-80.qza

Now I want to see what sequences clustered together in an OTU. I.e., I have a list of representative sequences for each OTU, I want to see what other sequences belong to that OTU other than the representative sequence.

I have not been able to do this with Qiime nor Qiime2, but the usearch tool (natively) had an option to map all reads to the Representative sequences and create both a mapping file and an OTU table. Is there such an option with Qiime2?

Thanks!

[Nicholas_Bokulich]

Welcome to the forum, @Maryam!

@Maryam

the usearch tool (natively) had an option to map all reads to the Representative sequences and create both a mapping file and an OTU table. Is there such an option with Qiime2?

As you noted, QIIME 2 will output the OTU table and representative sequences, but currently does not have a way to make this "OTU map" that maps the input sequences to the representative sequences in the output. We have an open issue to add support for this but I do not have an ETA on when that feature will be added.

[Maryam (Maryam Elfeki)]

Thank you for the welcome Nicholas, and for the reply!