denovo clustering from DADA2 table and rep-seq

[steffi]

Dear All,
Ive samples from multiple sequencing runs. hence I ran nf-core amplicon sequencing pipeline and got table.qza and rep-seq.qza files. These are ASVs. I also need OTU table. So I need to run OTU denovo clustering. I checked this post and they mentioned that I can give table.qza and rep-seq.qza as input for OTU denovo clustering. http://www.programmersought.com/article/2571545843/#_76

I would like to know whether is this right way to obtain OTU table based on de novo clusteriing

[kmz]

Hi,

Yes, that is what I do as well. But I set percentage identity to be 0.975 (because I believe 97.5% similarity is the standard for getting OTUs). But you can set it it whatever you need.

When I have multiple sequencing runs, I generate the OTU tables (eg table-dn-99-1.qza and table-dn-99-2.qza) for each sequencing run, and then merge these.

Good luck!

[steffi]

Hi Thanks for the reply.
Since I run nf-core multiple sequence run, I already have combined table.qza and rep-seq.qza.

So I used above as inputs for denovo clustering using vesearch adn I set the cutoff 97 percentage.

Thank you again