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Hello!
I used UNITE to assign taxonomy.
When looking at the assignments some received:
- OTU_6 k__Fungi NA NA NA NA NA NA
- OTU_4 k__Fungi p__Fungi_phy_Incertae_sedis c__Fungi_cls_Incertae_sedi…
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Tool users supply a taxonomy file when the data is processed by the tool to generate a dwc-a. Ideally, the `scientificName` is either a BIN, SH etc. and it is possible to include Linnean ranks with fu…
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Hi!
I'm using the 16S-wf in the Epi2Me desktop application. I typically have full 16S reads and use the NCBI database that is provided in the workflow and minimap2 to assign taxonomy at species leve…
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I think it would be good to have an option to train a new IDTAXA (or any other classifier we end up using) model if only a FASTA file is provided. This will make freyr more self contained, and allow u…
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Hi,
Im looking to get consistent results per samples such that sample X in cohort A will have the same results as the same sample X in cohort B.
I have previously run dada2 (stand alone) on coho…
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First of all, diamond is a great tool, thank you for building and maintaining it!
I run into a weird issue while working with a custom, Genbank-derived sequence and taxonomy database, namely that the…
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Hi @benjjneb this isn't an issue with dada2 but more a general question. We're using a slightly modified version of the big data workflow implemented in Nextflow for processing PacBio data, but the k…
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I am analyzing ITS1 amplicon data using DADA2 and the UNITE reference database. Last week I had an issue where the assignTaxonomy function was labeling ASVs as outlandish taxa (telling me I had marine…
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Hello! I was using this package to generate OTU assignments and to understand the communities for a set of metagenomic raw reads that I have. While converting the table to a wide format suitable for p…
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In running a CONSTAX job on the MSU HPCC there were some strange results in taxonomy assignment. For details I do have to give that I suspect may be relevant, I had the job train using the UNITE gener…