step by step tutorial specifically for qiime2-amplicon-2024.10

User Support
1

Thank you for the step bu step tutorial.
I am very new in Qiime2, and starting to migrate to the amplicon mode.
I am not sure if I should do all the steps of the testing with greengenes, or stop after dereplicating after extracting for the region I am sequencing V3V4.
Also , is there a step by step tutorial specifically for qiime2-amplicon-2024.10
Thanks
Eugenia

2

Hi @EugeniaSH,

I assume you are referring to help locating tutorials for amplicon sequence data?

There are several places you can go to learn more:

-Cheers!

1 Like
3

Thanks,
I have previously done the tutorials of "moving pictures", but it is based on the more general Qiime2, not the specific new qiime2-amplicon-2024.10
I am particularly stuck there, since I would like to use the new Silva taxonomy 138.2 , and I am not clear how to transition from qiime2-2022.

thanks
Eugenia

4

I am not sure what you mean ... The general approach of processing / analyzing your data has not changed between versions. The second link takes you directly to the 2024.10 tutorials page.

If you'd like use SILVA 138.2, you can simply replace the taxonomy reference files presented in those tutorials with the updated ones. You can RESCRIPt to generate the SILVA 138.2 files as generally presented here. Again, you can curate as you like, i.e. skip / modify the commands as needed.

The easiest way is to simply install a new QIIME 2 2024.10 environment as outlined here. Then activate that environment and proceed as normal using the tutorials.

Does this help?

5

Thanks,
appologies for the super basic questions.
I followed the tutorial of the RESCRIPT , not sure where to stop and which of the outcome files .qza to use.

For my final taxonomy classification I use this script
qiime feature-classifier classify-sklearn
--i-classifier /classifier.qza
--i-reads rep-seq_EXPERIMENT.qza
--o-classification taxonomy_EXPERIMENT.qza
qiime metadata tabulate
--m-input-file taxonomy_EXPERIMENT.qza
--o-visualization taxonomy_EXPERIMENT.qzv \

here the classifier.qza I am using : silva-138.2-ssu-nr99-515f-806r-classifier.qza from (https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database)

and then the bar plot
qiime taxa barplot
--i-table filtered-table.qza
--i-taxonomy taxonomy_EXPERIMENT.qza
--m-metadata-file Metadata-EXPERIMENT.tsv
--o-visualization taxa-bar-plots_EXPERIMENT.qzv

Thanks a lot for the help
Eygenia

6

It appears you are doing things correctly. You can use either the full classifier or the amplicon specific classifier on your data. Then use this for a variety of things, like visualize a barplot (as you've shown), create a PCoA biplot, collapse your features by taxonomy, etc...

It depends on what you'd like to do for your analyses.

This link is broken... not sure what you're referring to here.

7

Thank you very much.