Manual assignment of ASV after BLASTing

[callmcgovern]

Hello, I have been running a microbial community analysis through the dada2 pipeline and it has been working well however when I go to assign taxonomy I notice that my top 3 most abundance ASVs are being assigned to "Tychonema" but when I blast the ASV on Genbank I am seeing "phormidium autumnale" as a 100% match. Is there a way I can manually change the taxonomic assignment from tychonema to phormidium? The samples are benthic and, based on our in-culture experiments, we are pretty sure it is truly a phormidium, not a tychonema (which is usually planktonic). Thank you so much for the help.

[benjjneb]

Is there a way I can manually change the taxonomic assignment from tychonema to phormidium?

Yes, you can just use base R to manipulate the taxonomy table returned by assignTaxonomy. That table is just a character matrix, and you can overwrite the values in the appropriate cells to your hand assignments. For example:

## asv1 is the sequence of asv1
tax[asv1, "Genus"] <- "Tychonema"

[callmcgovern]

Thank you very much Ben, this helps a lot!