So my question is, which table.qza and rep-seqs.qza should we choose when we want to begin a picrust2 analysis? The two after the culster-features-closed-reference (table-cr-97.qza, rep-seqs-cr-97.qza) or the two finished the chimera filtering(table-cr-97-nonchimeric-wo-borderline.qza, rep-seqs-cr-97-nonchimeric-wo-borderline.qza)?
Not mean to disturb, just feel confused, hope you can help me.
This plugin can be integrated with the output files of the default QIIME2 pipelines - i.e. with denoising approaches rather than closed-reference OTU picking.
They are talking about the ASVs made by dada2 from this part of the Moving Pictures Tutorial.
But it looks like you using vsearch to make your features, and picrust2 supports those too! So I would recommend using the same sequences and tables you use for the rest of your analysis.
@colinbrislawn Thank you for your reply! But I think I didnโt make the question clear.
My question is: I want to use the .biom and .fna file to do the Picrust analysis, is it necessary for me to use the .biom and .fna file generated by closed reference + chimera filtering, or I can just use the .biom and .fna generated by closed reference (without chimera filtering), or the two kinds of .biom and .fna are both ok?
By the way, I want to use the dada2 pipeline, but I donโt have the .fastq file, I only have .fna file . I have no choice but to use vsearch.
Can I understand the sentence as following: Closed-ref works according the database, so I don't need to remove the chimeras from the table and ref-seqs generated by closed-ref, no matter what analysis I want to do in the next step (classification or picrust analysis).
In contrast, de novo and open-ref ask us to do chimeras removing, no matter what analysis I want to do in the next step (classification or picrust analysis), right?