I have been attempting to create a 16S rRNA analysis pipeline that uses de novo otu picking, using mostly Qiime. The pipeline that I am using does not ever output the actual Greengenes identifiers that are referenced when assigning taxonomy to my otus that are defined. Is this standard in de novo otu picking? For some functional as well as some tree creation, I would need those Greengenes identifiers, so does this mean that to do analyses, such as PICRUSt, that I would have to do an open reference otu picking method?
1 answer
How could you get GG ID's with de novo OTU picking since reference is never used? You're picking OTUs de novo. And yes, you would have to use closed or open reference OTU picking to get the identifiers. Alternatively, I imagine you can somehow assign IDs to your de novo OTUs post OTU picking.
Log in to answer this question.
-
Multiple taxonomy hits per OTU ID in VSEARCH despite --top_hits_only (90% ID after QIIME2 clusterin…
written by salma.sarker •
-
ERROR RAISED DURING STEP: Assign taxonomy
written by pasha64t •
-
How reads are divided into taxonomy level in Qiime?
written by agata88
-
Using FastTree to Constrian by Taxonomy
written by dmj6ab •
-
Identify OTU to species by using MOTHUR
written by liqing1123 •
-
UniFrac in R with just the OTU table?
written by David
-
Convert biom to tabular file and parse taxonomic levels
written by naphtali.paul •
-
High % of NA OTUs after assigning taxonomy (QIIME)
written by spencer.crook •
-
Making custom database (like green genes) for QIIME Closed-reference OTU picking
written by arnstrm
-
Mixing Barcode Lengths 16S
written by c.v.oflynn
