Downloading metadata for taxonomy

Hello,

I am wondering what is the best way to download metadata for making a barplot:

First I use this command which works fine:

qiime metadata tabulate --m-input-file taxonomy.qza --o-visualization taxonomy.qzv

Then I view the file:

qiime tools view taxonomy.qzv

A window opens in Firefox and there is a button at the top that says "Downlaod metadata TSV file"
When I click on the file the actual text appears instead of a file being downloaded.

Should I copy all the text and try to save it as .tsv?
Would using a different browser work?

I believe I need this metadata in order to run the following:

qiime taxa barplot --i-table table.qza --i-taxonomy taxonomy.qza --m-metadata-file --o-
visualization taxa-bar-plots.qzv

Thanks in advance,

Andrew

Hey @Andrew_Richards,

The issue you’re having with the file you want to download showing up as text is probably just the setting on your Firefox Browser. The same way you can change whether .pdf files should be opened in a browser viewer vs. download to disk. Not sure where exactly this setting is but dig around yourself or google it I’m sure you’ll find it.
That being said, for what you are trying to do, which is to use taxa barplot plugin you don’t actually need to download anything. The metadata that is needed here is not related to anything in your taxonomy.qza, but rather it refers to the sample metadata. In other words, you already have all the data you need. In your --m-metadata-file parameter, simply put your sample metadata file, which is the .tsv file that you probably made in a previous step that holds information about your samples (ex group designation, source, date, etc…). This is not something you need to extract from a qiime2 artifact.

This is what your command should look like

qiime taxa barplot \
--i-table table.qza \
--i-taxonomy taxonomy.qza \
--m-metadata-file metadata.tsv \ #or whatever your metadata file is named
--o-visualization barplot.qzv 

Have a look at the barplot section of the Moving Pictures tutorial for a more detailed example workflow.

Hope that helps!

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@Mehrbod_Estaki Thanks for clearing that up. I was able to get past that issue by using view.qiime2.org but now I have run into something else.

The problem is I don’t have a metadata file. I did not get anything from the sequencing facility besides the fastq files. I have read the metadata tutorials and visitied the keemei verification page and it is quite easy to make one, however I am afraid that the facility no longer has the barcodes associated with the samples.

I was able to skip the metadata because it is optional in the following command:

qiime feature-table summarize —i-table table.qza —o-visualization table.qzv —m-sample-
metadata-file metadata.tsv

Any advice on this would be appreciated.

Thanks

1 Like

Hey @Andrew_Richards,

Good! Remember, any visualization artifact (those ending with .qzv) are viewable on view.qiime2.org and will have an interactive visualization component. Even the .qza artifacts are viewable however those will only show the artifacts type and provenance and will not have an interactive component. You may want review the core-concepts tutorial as a refresher.

As for your metadata file, you do NOT need barcode information here. In fact, you are well past this point since you already have your feature-table and taxonomy files etc… Barcode information is only relevant if you are starting with raw multiplexed files. So this metadata file just needs to have information relevant to your experiment set up.

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