My libraries contain reads from _two_ variable regions - how can I proceed with the analysis?

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Hi @bmb22!

So you want to analyze data from both regions together? Some notes:

  1. Have you seen this topic thread?

  2. You basically have three options.

  3. See also this thread.

  4. Sounds like you have a job for q2-fragment-insertion.

Or do you just want to separate out the different variable regions to analyze separately, since they were combined by mistake? If so:

  1. Use extract-reads to trim your reference sequences to the different variable regions
  2. Use exclude-seqs to select the genes that align to each variable region within some % similarity (I am not sure what is a good setting for this, but the different variable regions are probably dissimilar enough that you can be fairly flexible with this).

That should split them out sufficiently.

I hope that helps! Let us know if you have any more questions.

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