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I need to reassign an errant phylum assignment given by greengenes. I simply need to reassign (replace) the phylum "Tenericutes" to "Firmicutes". How can this be done within phyloseq?
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Currently the documentation instructs and the code downloads `prot.accession2taxid.gz` which doesn't have all of the `nr` accessions.
Proteins that aren't found in `prot.accession2taxid.gz` are assi…
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Hey there, @shenwei356 :)
Thanks again for not only additional wonderful software, but excellent documentation as usual!
I'm looking for a better way to taxonomically classify predicted coding …
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Hello, We've performed Metannoatae on big metagenomic file(translated) against hmm of interest. Though we got the results, more than 99% remained to be assigned.
![canvas](https://user-images.gith…
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Below is the complete output of a run I did last night. There are several errors in the output:
* Partial codon
* invalid value encountered in double_scalars (twice)
* RuntimeWarning: divide by z…
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Dear Emese,
First of all, thank you for creating this tool and the documentation. They are really helpful. I created a custom database to use with the blast+ command line utility. However, the result…
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Add the taxonomy to facilitate things like:
- annotating internal nodes with taxon names
- cross-referencing nodes from different trees on the basis of taxon assignment
- identifying percent taxonomic…
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I downloaded refseq database and run kaiju for taxonomic assignment of sample DRR496098 downloaded from SRA, in the kaiju/bin directory using the command below;
./kaiju -t ../../kaiju_db/nodes.dmp -f…
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Hello,
I am using kraken2 to assign sedaDNA reads to a custom database (made of mitochondrion and chloroplast genomes).
I had to redo some sequencing and my project quite go running through time w…
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Hello,
The taxonomy_assignment_BLAST_V2.py script works great for taxonomic assignment using default parameters. However when I use it with the filtering option "length_percentage" with values equa…