Associating a representative sequence/feature ID with samples that have that sequence

General Discussion
#1

Hello!

Two questions, actually:

  1. When I get representative sequences/feature IDs after doing a vsearch, is there a way to associate a resulting sequence with the sample or samples associated with that sequence? For example, I have a feature ID that comes back as Wolbachia-- can I then determine exactly which of my samples have that sequence of Wolbachia in them?

  2. Assuming that I can accomplish #1 above, is there a way to quantify how many reads within a sample are associated with the sequence?

Thank you for your time!

Best regards, Brian

#2

Hi @l.brian.patrick,

Yes!

You should have a feature id (let’s use :dog: because it’s as easy as anything else). This feature ID should appear in your taxonomy artifact:

Feature ID Taxonomy
:dog: k__Bacteria; p__Proteobacteria; …

It will also appear in your representative sequences:

Feature ID Sequence
:dog: CATCATCAT

And, in your feature table (lets name our samples :woman_artist:, :woman_astronaut:, :woman_technologist:)

Feature ID :woman_artist: :woman_astronaut: :woman_technologist:
:dog: 0 1 100

You may want to look into the filtering tutorials specifically to see how to extract the features you want.

Best,
Justine

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