exporting taxa-bar-plots.qzv into Excel

Hello,

I am currently trying to export my data from the taxa-bar-plots.qzv into Excel. I saw that there is the option to export it as a CSV file. But I am not sure how to read this file in Excel. I have all my assigned Taxa in the first row and then my Samples with a lot of numbers (which I am not to sure what they stand for) in the following lines.

image

My question is if it is possible to get an easier overview of my data and if I am able to see the Barcodes of the matching Taxa somewhere?

Thank you so much in advance.

Hi @Clarissa,

You should have various import options when opening a file in excel, e.g., to read a file as comma-delimited (CSV, what you have) or tab-delimited. Usually excel reads CSV by default, but you may need to adjust your column delimiter option when opening your file. The options for MS office software tend to vary widely by version, so you should probably just do a web search and/or search the MS Excel docs for info on opening CSV with excel.

Those numbers are the number of times each taxon was observed in each sample. This is the total number of sequences attributed to that taxon, not relative frequency.

You can use qiime taxa collapse to collapse your feature table by taxonomy, then use qiime metadata tabulate to view a feature table in a searchable format. That will allow you to look at counts of individual taxa in your table, if you want an equivalent “excel-style” view.

No — the barcodes are long gone at this point (assuming you are talking about the unique barcodes assigned to each sample for multiplexed sequencing?).

If by barcodes you mean the sequences themselves, metadata tabulate allows you to merge sequences and taxonomy together in a table:
https://docs.qiime2.org/2020.6/tutorials/metadata/#exploring-feature-metadata

I hope that helps!

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Hi @Nicholas_Bokulich and @Clarissa,

One other potential (and delightful!) CSV problem is that CSV doesnt mean the same thing in every country. A us-based system (like :qiime2:) puts out a csv that uses a comma (,) to seperate characters and a period (.) to indicate decimals. so, like,

animal, goodboy-ness-dec
dog,  1.1
cat, 1.0

In at least some european countries, the format uses a semi colon (;) as their delimiter and a comma (,) as their decimal

animal; goodboy-ness-dec
dog; 1,1
cat; 1,0

There are two solutions to that particular and delightful problem. One is to use a tsv which seem to be pretty universal in my somewhat limited experimentation. Two is to change the configuration of your system (which is what I did because Im obnoxiously :us: when I do computation)

Im not sure if this is the actual problem, but its something to be aware of in the file.

Best,
Justine

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You were right this worked, thank you very much!!

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