Moderator: 5heikki
5heikki ♦ 8.9k
- Reputation:
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- Finland
- Last seen:
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- Joined:
- 6 years, 7 months ago
- Email:
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Posts by 5heikki
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... SPAdes assembler is from Algorithmic Biology Laboratory Russian Academy of Sciences, St. Petersburg Academic University. Can't be that bad.. ...
written 3 days ago by
5heikki ♦ 8.9k
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... That's not a mislabeling, SARS-COV-2 is under that taxid
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=694009
NCBI taxids are hierarchical, e.g. humans are under many different taxids: eukaryotes, animals, chordata, mammals, etc. ...
written 3 days ago by
5heikki ♦ 8.9k
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... 1. Make sure you don't have the results file open in Windows (e.g. reboot)
2. Delete the results file
3. Confirm with ls that the results file no longer exists in that dir
4. Run your script ...
written 7 days ago by
5heikki ♦ 8.9k
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... > I think for being a moderator once should have a specific degree. Otherwise what is the use of higher degree, like PhD
I would like to think that people have better reasons for doing a PhD than just being qualified to remove male enhancement spam from biostars :D
P.s. Your dismissive attitude ...
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... How is it possible to have two files with the same name in the same directory? ...
written 8 days ago by
5heikki ♦ 8.9k
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88
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... Assuming you have e.g. filtered away singleton reads prior to clustering, why do you feel like you need to filter your OTU table at all? ...
written 11 days ago by
5heikki ♦ 8.9k
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... This can be done by piping GNU parallel to e.g. awk or sed. I don't have an access to a terminal right now but basically just following [this][1]
[1]: https://www.gnu.org/software/parallel/parallel_tutorial.html#Multiple-input-sources ...
written 17 days ago by
5heikki ♦ 8.9k
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... No need to assemble, just map the reads on to a reference genome and extract the consensus sequence. If everyone did like this the gisaid dataset would be of much higher quality.. ...
written 19 days ago by
5heikki ♦ 8.9k
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... This can be done very quickly with [Mash][1]. Read the docs and the paper and marvel how great stuff MinHash and representative sketches truly are. ANI is approximate to one minus Mash distance..
[1]: https://mash.readthedocs.io/en/latest/ ...
written 22 days ago by
5heikki ♦ 8.9k
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... There is no such file. You will have to do it the same way everyone else does it and download the genomes separately. You can parse the ftp addresses from the assembly summary files. All RefSeq bacteria is 600-700GB and all GenBank bacteria +1TB. Generally you would want files which fit on the RAM o ...
written 22 days ago by
5heikki ♦ 8.9k
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For C: Finding a sequence in a fasta file
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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For A: NCBI API for finding accession numbers?
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For C: Finding a sequence in a fasta file
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For #saveNCBI - it's a joke, right?
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For A: NCBI API for finding accession numbers?
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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For C: Finding a sequence in a fasta file
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
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For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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