Hi there.
I have got my feature table using the dada2 algorithm, then I exported and merged it with the taxonomy annotation file obtained from sliva_128 release. The out_id in the OTUID column looks something like “01fe2ad4c2e075979225a4966bb8137a”. How can I convert it into genbank accession number(eg: “EU722746.1”) so that i can search the database.
Thanks!
Hi @pixar,
Those sequence IDs are unique for each given sequence variant, so allow for comparison of exact sequence variants between studies that use the same exact methods.
Sounds like you are trying to do taxonomy assignment? You can use the various "classify" methods in q2-feature-classifier against a reference database of your choice.
E.g., you can use a BLAST-based classifier, or use a naive bayes classifier implemented in QIIME2.
The QIIME2 website contains links to various compatible databases. You could download a set of genbank sequences, reformat to match those compatible references, and use that custom database for searching.
Alternatively, if you are interested in searching for specific sequences against genbank, use qiime feature-table tabulate-seqs as shown here. The output provides streamlines searching genbank for individual records if you really want to pick through (use feature-classifier against a custom database if you want to classify all sequences to taxonomy)
Let me know if that's what you're looking for!
Yes, I’m looking for methods to search interested sequence against genbank, I forget the rep-seq.qzv artifact. Thanks a lot!
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