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I did some poking around with respect to HCV, GlyGen, and the NCBI Taxonomy:
* HCV-H glycans are from dataset GLY_000335, which provides the uniprot
tax id as taxid 63746. This is NOT a species, s…
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Dear Dr. Lind,
I'm generating a custom eukdetect db and I'm stucked at get_uncomputed_taxid_per_busco.py. It fails with the following message:
"""
python /home/qi47rin/proj/00-git/EukD…
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the GlyGen team had a meeting and decided on the next species we would like to add to GlyGen over the next few releases:
* Bovine (2.7)
* Zebrafish / Hamster (2.8)
* Rice (2.9)
The number in par…
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Start searching primer for Bacillus_subtilis
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fatal error while working on Bacillus_subtilis check logfile /home/cberruto/speciesp…
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Should be a double query:
- one on the taxid
- one on the sciname if the species has no taxid in wikidata
See what identifiers to get back.
See also #6
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Hi all,
Thanks so much for your wonderful works.
I have download s pre-built kraken2 database (PlusPFP) from https://benlangmead.github.io/aws-indexes/k2. However, some taxids in this database d…
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Hello, may I know how to configure to return taxid and taxname?
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Hi, I noticed that some converted gid has taxid -1. I think the problem is related to the process of removing GI numbers from the presentations of nucleotide and protein sequence record. These gids ar…
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Hi everyone
I'm writing this here in hope that someone will solve this issue as this is already an unsolved issue as per the thread, https://github.com/DerrickWood/kraken2/issues/291
So, I fac…
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> Given a list of binomial names, how can I get accession ids and sequences?
```
For each database in ['plant', 'vertebrate', 'invertebrate] do
taxids = restez::list_db_ids() |>
restez::gb…