see the content of feature table.qaz

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1

Dear All,

Is there any way to visualize or see the content of feature table.qaz.

Thanks,

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Hi @gjahanmir,
You will want to run qiime feature-table summarize!
Have you checked out our tutorials? Our tutorials have all the initial commands that are good to know! “Moving Pictures” tutorial — QIIME 2 2023.9.1 documentation

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HI @gjahanmir,

Here is one approach to visualize the actual feature-table, with the option off adding taxonomy, if you have it.

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6

Dear @cherman2,
Thanks for your help and prompt reply. I tried this one. The results are some statistics about the feature-samples and frequency bar plots, but I want something like whole raw data in a table format.
Rows are samples and columns are gene variant frequencies.
is it possible?

thanks and Best Regards,

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Dear @SoilRotifer,
Thanks for your reply. Can you please elaborate more on this?

Thanks,

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Hi @gjahanmir,
It looks like @SoilRotifer solution would be exactly what you want. Did you run the commands that he linked? That will give you a visualization that will enable you to look at the feature table as a table. You might want to skip the transpose step if you want the rows as samples!

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Dear @cherman2,
thanks. Yes I tried, but I am not sure when I do not include the transpose code, how could the software understand to do data arrangement on the table.qaz in the next code lines. Because feature table is input of qiime feature-table transpose only.

qiime feature-table transpose
--i-table table.qza
--o-transposed-feature-table table-transposed.qza

qiime metadata tabulate
--m-input-file table-transposed.qza
--m-input-file taxonomy.qza
--o-visualization counts-and-taxonomy.qzv

I am using data from this link
GitHub - Gibbons-Lab/isb_course_2020: Materials and tutorials for the 2020 ISB Microbiome Course.

The transposed feature table I got, has 443 id(as feature). I think it is the thing I want but I am not sure how to confirm this 443 ids if it is correct or not.

Thanks again,

10

If you are following the standard QIIME 2 approach of generating a feature-table, you'll have to transpose the table, only if you are going append taxonomy, or other metadata, that is being joined on the feature-id. The transpose command does not know anything about your data, it will just transpose the table it is given. If you are unsure of which orientation your feature-table is currently in you can simply run the following to see which way the data is oriented:

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

From this you'll see that the rows are samples, and the columns are feature-ids. But if we'd like to append other metadata, like taxonomy, to this table we need to transpose the table so that the rows are feature-ids and the columns are samples. This way we can append the taxonomy, and other metadata, which are joined to the table via the row (feature-ids).

This should match the information output from:

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

-Mike

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@SoilRotifer

Thanks a lot.

The following code produced exactly what I was looking for.

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

Thanks again.

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