Daniel Straub
Daniel Straub
I see. The outdated taxonomies could be probably improved that way. Regarding comparing it with whole genome-based methods, one could either use GTDB via `--dada_ref_taxonomy gtdb` (the corresponding shotgun metagenomics...
Databases are non-trivial to compare, so if you do not find a "crucial" taxa, turn to another one. Another reason could be that classification with DADA2 is not always same,...
I am benchmarking currently, hope that will shed some light on it.
Hi there, I agree that would be nice. If you are up to it, make a PR ;)
This is in dev and will be in the next release, 2.10.0!
I think metdata is not required by the function that produces barplots. However, the pipeline requires it, thats a relict of the past when metadata was indeed necessary for producing...
This is in the dev branch and will be in the next release.
@WangLab-SCSIO did that or any other procedure resolve your problem? If yes, please give feedback and close the issue. If not, please also let us know.
I close that issue now because of missing response. Feel free to open it again in case you continue to have the issue.
Hi @ShareiFae , emu seems indeed interesting, its also available as container https://bioconda.github.io/recipes/emu/README.html. However, if I understood correctly, it compares sequences to a database and makes count tables from that....