q2-vsearch! how can i get seq.fna with qiime2? please save me ! i have nothing to do

in the picture above, seq.fna is got from qiime1, so when i use qiime2, how can i get the seq.fna?

do i need to run dada2 and deblur to get the feature-table.qza and rep-seqs.qza?

Yes! Then you can export your data as shown here: https://docs.qiime2.org/2019.10/tutorials/exporting/

Yes. Then you can open up up the .qza files. (They are just .zip files, so you can rename them and reopen.)

thanks for your solution! and what puzzle me is that i have got the otu table(feature-table.qza),and i need to use the gotted otu-table as a import qza to clust to get another otu-table(if i run De novo clustering or Open-reference clustering), is there something weird? as the photo below showed, the import qza is a raw demux seq from vsearch' derepricate operation.so is it appropriate when a denosied otu-table serve as a import file of vsearch' cluster.


Hey Rick,

That’s right; first you dereplicate, then you cluster. Dereplicate is essentially 100% clustering, so you get rep set and a table, just like if you clustered at 97%.

Sure! We recommend doing denoising (like dada2) first, then clustering if you really want 97% OTUs. Keep in mind that you need both inputs, both table and sequences.

Colin

2 Likes

Oh my ! Colin, you dont know how much assistance you have gived me! I am so thankful for your patience and detailed reply! it help me a lot ,really. this problem have puzzled me for many times. and i think i can understand it now, even i dare not say i am fully know the theory. but i can go to practice and operate my otu-table and rep set, that is wonderful and stunning for me. thanks for you again.

2 Likes