Converting .qza to .qzv files for visualization in vsearch cluster-features-closed-reference

Hi, I have what is probably a very basic question on converting .qza files to .qzv.

I was trying to go through the steps in this thread for closed-reference OTU picking using my DADA2-generated table. I am trying to convert the 3 resulting .qza files (unmatched_sequences.qza, clustered_table.qza, clustered_sequences.qza) to .qzv files for visualization (like in this post so I can determine the % of unmatched sequences), but it seems like the --o-visualization option is not an option with the qiime vsearch cluster-features-closed-reference command.

Any help in converting these .qza files to visualizations would be greatly appreciated!

Good morning,

Thanks for linking to that thread. Based on what I see in that thread, all the graphs they show are made in MS Excel and not from a Qiime2 visualizer.

You can return unmatched sequences by using --o-unmatched-sequences or by passing --output-dir like @jjmmii did. Then you make graphs of that data using any program you want, like MS Excel or Google Docs.

I hope this helps answer your question. There is now way to make a .qzv file, but you can visualize it with another program!

Colin

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Hi @colinbrislawn, thanks for your response. I was wondering how @jjmmii generated the .qzv files referred to in the response to the post, i.e.,

or perhaps the better way to look at the (unmatched_sequences.qza, clustered_table.qza, clustered_sequences.qza) files is to export into .tsv?

Thanks!

Hi @colinbrislawn, while that is certainly one option, it isn’t the only one available to @slh277!

  • You can summarize any FeatureTable[Frequency | PresenceAbsence | RelativeFrequency] (in your case clustered_table.qza)
  • You can tabulate-seqs on any FeatureData[Sequence] (in your case, unmatched_sequences.qza and clustered_sequences.qza).

Hope that helps! :t_rex:

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Thank you @thermokarst!!

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