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**Improvement Description**
I thought about the `FeatureData[Taxonomy]` artifact and Daniel's warnings about the quality of the assigned taxonomic labels, which depend on the quality of the placement…
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How to do Preprocessing and filtering of the phyloseq object all these following three criteria
1) taxa with zero counts;
2) taxa with ambiguous taxonomic assignment at the Kingdom or Phylum le…
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The first time I used R taxonomy I noticed some different "dropped" patterns than the standard eDNAFlow typically provides. Here is a summary of taxonomic assignment at all levels with R taxonomy:
23…
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# AMBER: Assessment of Metagenome BinnERs
_"AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It …
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Hi all,
Is there an excel template besides the nutritional one that is available here?
Preferably one with taxonomic assignment - i.e.; OTU's assigned to Order/family/genus/species - with similari…
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I have run into an interesting situation when comparing assignments between nucleotide and protein databases. My databases contain NCBI bacteria, fungal, and human sequences built using kraken2-build …
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I keep seeing the presence of an unknown taxa with the name "V1" anytime I construct my taxa bar plots. However there is nothing in my taxanomy.tsv file that traces back to this "V1" taxa and it seems…
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Hello Ben and team,
I am having trouble with the taxa assignation using dada2 and the MIDORI reference database. I've sequenced a Metazoan COI library based on Leray et al. 2013 primers targeting an …
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Especially with eDNA data, there is a need for reliable, (possibly local?) genetic reference databases that are used for the taxonomic assignment of sequences. Is there a role that OBIS as a database …
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Hi Florent,
We are using the program with an input OTU table containing OTUs at a higher taxonomic rank, e.g 'Root; k__Bacteria; p__Planctomycetes; c__Phycisphaerae; o__Phycisphaerales' (order level)…