V4, V3-V4 amplicons feature-classifier-Silva138

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I am new to using the QIIME 2 classifier, and I have two different sets of 16S rRNA data: one from the V4 region (mouse) and another from the V3-V4 region (human). I would like to know the best approach for taxonomic classification in this case. Specifically:

  1. Should I train a custom classifier using the feature-classifier commands for each region, or can I use pre-trained classifiers available in QIIME 2?
  2. If pre-trained classifiers are recommended, could you provide guidance on where to find appropriate classifiers for the V4 and V3-V4 regions and how to ensure they are compatible with my data?
  3. If training a custom classifier is necessary, could you outline the steps involved, including any specific considerations for my mouse V4 and human V3-V4 datasets?

Additionally, I would like to compare both datasets by merging feature tables and taxonomies. Could you provide any advice or best practices for doing this effectively in QIIME 2?

Thank you!

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Hi @MSrinivasan,

RE 1 & 2:
I suggest working through this tutorial. You can use either pre-trained classifiers or ones you train yourself. It's up to you. :slight_smile:

If you search the forum you'll find additional content:

RE 3:
Please see the tutorials:

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I want to do the analysis for mouse vaginal microbiome its not usually present in V4 region 16s rrna amplification. I want to use NCBI Database for mouse vaginal microbiome, could I have to look on how to use NCBI database for the microbiome database
Thank you!

4

Hi @MSrinivasan,

If you search the forum you'll find these helpful threads. You can also checkout the RESCRIPt Tutorials.

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