Dear All,
Is there any way to visualize or see the content of feature table.qaz.
Thanks,
Dear All,
Is there any way to visualize or see the content of feature table.qaz.
Thanks,
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 2023.9.2 documentation
HI @gjahanmir,
Here is one approach to visualize the actual feature-table, with the option off adding taxonomy, if you have it.
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,
Dear @SoilRotifer,
Thanks for your reply. Can you please elaborate more on this?
Thanks,
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!
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,
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
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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