I was left with a doubt regarding the analysis of the ITS data, I am using Qiime2. After Decontam I would like to know if it is correct to use uchime to remove Chimeras as you describe in Identifying and filtering chimeric feature sequences with vsearch or not. Only the dada2 is suficient?
Excuse me if asking is simple, I am starting with q2 has little time.
Thank you for assistance
Welcome to the forum @aoliveira!
If you are using dada2, you do not need to use subsequent chimera filtering, as the methods in q2-dada2 include a chimera filtering step.
If you are using OTU clustering (following that q2-vsearch tutorial) instead of denoising methods, you should include a chimera filtering step. If you are using dada2 for denoising, there is no need to follow that tutorial, as it is for a different type of workflow.
This example — of denoising vs. OTU methods — is one example of how QIIME 2 hosts many different methods, and many different possible workflows. The wealth of possibilities can be confusing and overwhelming! While it is not an exhaustive tutorial, I recommend reading the “overview tutorial” and others at qiime2.org to get a sense of the different workflows possible for amplicon sequence analysis with QIIME 2, and how selection of different pathways (e.g., OTU clustering or denoising) have different recommended steps.
Thank you so much for your help @Nicholas_Bokulich
I used the “Denoising” method and the reading was complementary to understand that there is no single workflow.
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