I am trying to generate a table of features and their respective counts per individual sample, exactly like the CSV output from qiime taxa barplot but instead of a taxonomic affiliation, I would like feature ID’s - how should/could I obtain this file? The feature-table summarize gives feature frequencies across all samples, although how can I generate the per-sample breakdown of this? Surely it must exist somewhere?
You can try to export a feature table:
qiime tools export \
--input-path feature-table.qza \
And convert .biom to .tsv:
biom convert -i Biom/feature-table.biom -o Biom/feature-table.tsv --to-tsv
Output should be a tsv file with features and counts.
Hope that it is what you was looking for
Thanks a lot for the suggestion, however this is basically exactly what I have produced previously! This is what I am able to generate at the moment:
with the total feature counts per sample:
However, I would like to know the PER SAMPLE breakdown (individual feature abundance per feature per sample) of the features displayed in the above feature table, as they are given in the CSV file that can be downloaded after taxonomically classifying and visualizing (qiime taxa barplot), like below, only instead of taxa, I would have a feature ID and corresponding per sample abundance:
Is this something that can be produced? Any ideas?
Thanks again, awesome help though! Have a nice evening,
That is what @timanix shared with you above - the feature table is the per-sample breakdown of the individual feature abundances. The tables you have shared in your screenshots are summary tables of the feature table, but not the actual feature table itself. Please give @timanix's suggestion a try, here is a screenshot of the results:
You can also quickly run the following, if you just want to see the values:
qiime metadata tabulate \
--m-input-file feature-table.qza \
But, if you intend to perform some manipulations, calculations, etc, then the suggestion @timanix provided above is the right way to go.
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