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!
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!
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?
Hi @colinbrislawn, while that is certainly one option, it isn’t the only one available to @slh277!
- You can
FeatureTable[Frequency | PresenceAbsence | RelativeFrequency] (in your case
- You can
tabulate-seqs on any
FeatureData[Sequence] (in your case,
Hope that helps!
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