Moderator: 5heikki

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5heikki8.9k
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Posts by 5heikki

<prev • 1,201 results • page 1 of 121 • next >
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Answer: C: Russian universities for the study of biomedicine
... 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 5heikki8.9k
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Comment: C: Getting around wrong taxids in NCBI virus database
... 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 5heikki8.9k
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Comment: C: Script makes different file then the manual command, but the command is the same
... 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 5heikki8.9k
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Comment: C: SAVE biostars.org from FAKE and unnecesary answers
... > 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 ...
written 7 days ago by 5heikki8.9k • updated 7 days ago by Joe17k
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Comment: C: Can not work with a text file in script
... How is it possible to have two files with the same name in the same directory? ...
written 8 days ago by 5heikki8.9k
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Comment: C: filter OTU table based on absolute abundance
... 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 5heikki8.9k
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Comment: C: building all possible phylogenies.
... 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 5heikki8.9k
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Answer: A: How to extract genome from iontorent bam file?
... 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 5heikki8.9k
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Answer: A: ANI software for comparing large eukaryotic genomes
... 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 5heikki8.9k
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Comment: C: How do I download NCBI prokaryote Genbank and RefSeq databases as single flat te
... 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 5heikki8.9k

Latest awards to 5heikki

Commentator 7 days ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 19 days ago, created an answer that has been accepted. For A: NCBI API for finding accession numbers?
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Popular Question 3 months ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
Scholar 6 months ago, created an answer that has been accepted. For A: NCBI API for finding accession numbers?
Scholar 7 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 8 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 8 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 9 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 9 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Script for extracting data from a tab-delimited file
Scholar 16 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 16 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 16 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan

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