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Dies on subject sequence ID string with odd number of id|value pairs.
Why do we care about anything beyond the gi number? The database and accession (second pair) might come in handy, but only reall…
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### Operating System
Other Linux (please specify below)
### Other Linux
RedHat 7.9 (Maipo)
### Workflow Version
v2.9.0-gd9e8593
### Workflow Execution
Command line
### EPI2ME V…
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For example here I cannot pipe the whole thing together because of the tibble:
```
taxid ncbi_get_uid(db = "protein") |> ncbi_link_uid(to = "taxonomy")
taxizedb::classification(taxid$taxonomy)
…
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We are currently trying to use Single BaTS to produce a single treefile that is analyzing 2002 trees with 2 states. We have also tried an increased number of trees which has been unsuccessful. Our att…
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Hi, I'm having trouble running the workflow as instructed by the tool.
This is my command line used:
nextflow run /hpcfs/home/ing_quimica/v.rua/mettannotator -profile singularity --input /hpcfs/h…
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Try to list NCBI taxids that are not present in wikidata.
The sparql query to list taxids in wikidata is:
```sparql
SELECT DISTINCT ?ncbiId WHERE {
?taxon wdt:P685 ?ncbiId.
}
```
juba updated
2 months ago
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I'm building a database that I use with MetaEuk and I have taxonomy information but I'm not sure the correct formatting to use. Also, can there be missing fields to use the taxonomy feature? I have f…
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I'd like to use `diamond makedb` on a custom taxonomy created from the GTDB (via [gtdb_to_taxdump](https://github.com/nick-youngblut/gtdb_to_taxdump)). With diamond v0.9.30.131, I'm getting the error:…
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Hi,
I have been using Kraken2 to classify my 16S reads with the Silva and Greengenes databases provided, which works great.
I would like to compare the results to NCBI's standard 16S database as w…
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Hello!
I am relatively new to metagenomics and I've been using Kraken2 for my analysis. I was wondering if Kraken2 has some sort of way of removing DNA reads that do not belong to the sample analyz…