Can I turn fasta into qza for taxonomic classification?

Technical Support
8

There are a few ways to investigate this...

  1. :national_park: First, you can create a visualization of your feature-table with qiime feature-table summarize, and click on the 'Feature Detail' Tab at the top. This will list all the features and provide how many samples and how many times each feature appears in your data set. You can view the example on the QIIME 2 View page.

  2. :bookmark_tabs: Secondly, you can run the following command generate a tabulated view of your feature-table:

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

  • This will show you the features, as columns, and the number of times they appear in each sample. You can click on the "Download metadata as TSV file" tab if you'l like to view in Excel, etc... :box

  • :exploding_head: Bonus tip: You can combine this tabulation step with the qiime taxa collapse command. That is, collapse your features (i.e. combine them if they have the same taxonomy) first, then feed that output into the tabulate command. This will provide taxonomy, as columns:

qiime taxa collapse \
    --i-table table.qza \
    --i-taxonomy taxonomy.qza \
    --p-level 7 \
    --o-collapsed-table table-l7.qza

qiime metadata tabulate \
    --m-input-file table-l7.qza \
    --o-visualization table-l7.qzv

Optionally, you can transpose the feature table before making the visualization with qiime feature-table transpose.

  1. :triangular_ruler: Finally, if you would like a table along with it's taxonomy, you can export the table and append the taxonomy (i.e. old QIIME 1-like format) by following the instructions referenced here, or here.

Does this help?

-Cheers!
-Mike

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