Could my primers not have trimmed properly?
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2.3 years ago
k-vincent • 0

Anyone have any thoughts on what could be going on with my dataset? I'm relatively new to bioinformatics, so any advice is much appreciated!

I'm using the DADA2 pipeline and the UNITE database for assigning taxonomy to ITS data. The taxonomy resolution has been suspiciously low and I'm starting to wonder if the primers weren't completely trimmed in the cutadapt step.

A few questions:

  1. All my sequences start with CATT... is that normal?

  2. I BLASTed a few of the sequences with taxonomy assignment only down to kingdom and would sometimes get split coverage like this: https://ibb.co/bryQZ02 What's going on?

  3. If you have a sequence with low BLAST coverage and only a taxonomic assignment of Kingdom from UNITE, do you keep it or drop it (likely artifact?)? https://ibb.co/RN6czDh

Let me know if more information would be helpful and thank you in advance for your time!

ITS Trimming Primer DADA2 • 396 views
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