Can you enter the pipeline at feature table point?

I am trying to use QIIME for ancient DNA metagenomic analysis and normalizing and I’m wondering if I can enter at the feature table point with BLAST or Kraken based data? We have a specific pipeline for dealing with short, damaged reads so I would prefer to keep that upstream process and then enter into QIIME2.

Welcome to the forum @jessica_h ! Sounds like an exciting project!

Yes! You can definitely import your data into QIIME 2 at any point. There is an importing tutorial at qiime2.org that describes how to import all sorts of data types… and if you don’t see your data type there, get in touch on the forum and we can help figure it out.

You will need your feature table in BIOM format — then follow the instructions for importing biom-format tables in the importing tutorial at qiime2.org. This one:
https://docs.qiime2.org/2019.10/tutorials/importing/#feature-table-data

qiime tools import \
  --input-path feature-table-v210.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path feature-table-2.qza

What format do you have the taxonomy data in? If it exists as feature metadata in your biom table, you import the table a second time but specify the --type as FeatureData[Taxonomy] and the taxonomy information will be parsed from your table.

qiime tools import \
  --input-path feature-table-v210.biom \
  --type 'FeatureData[Taxonomy]' \
  --input-format BIOMV210Format \
  --output-path feature-table-2.qza

If it exists as a TSV file like this:

feature-id taxonomy
feature1 blahblahblah
feature2 blahblah

Then follow the importing steps in this tutorial to import the taxonomy:
https://docs.qiime2.org/2019.10/tutorials/feature-classifier/

But if the taxonomy is just the feature IDs in your table, then don’t do anything at all, just import the table as described above :smile:

You should make a QIIME 2 plugin for this! Then you can share your pipeline with the world, and your processing steps will be stored in provenance in all your QIIME 2 outputs. q2-ancient-dna :t_rex: :dna:

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Thanks so much for explaining.

I am new to this…I made a BIOM table in Version1 JSON format using kraken-biom and I am not sure if I need to do more than import the table using the code provided.

qiime tools import
–input-path feature-table-v210.biom
–type ‘FeatureTable[Frequency]’
–input-format BIOMV210Format
–output-path feature-table-2.qza

It looks like a shouldn’t need to as kraken-biome stores it in the biom table “Currently the taxonomy for each OTU ID is stored as row metadata in the BIOM table using the standard seven-level QIIME format: k__K; p__P; … s__S”

I have done the biom summarize option one my table and it says there is no sample metadata but there is taxonomy metadata

So to import the taxonomy follow the second import command that I posted above. So you import the same biom-format table twice: once as a FeatureTable[Frequency] and again as a FeatureData[Taxonomy].