User: oddjobs

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oddjobs0
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Posts by oddjobs

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Comment: C: Find all NCBI taxids in some group (e.g., all coronaviruses)
... I see. Thanks. It's nice to have in script form as my goal is to use this in a script in the end. The ncbi-genome-download tool also seems quite useful. I will look up both. ...
written 11 days ago by oddjobs0
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Comment: C: Find all NCBI taxids in some group (e.g., all coronaviruses)
... Thanks! I wasn't aware of this utility before. It will probably be helpful for other things I want to do as well. ...
written 11 days ago by oddjobs0
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Comment: C: Find all NCBI taxids in some group (e.g., all coronaviruses)
... That's probably the closest I can get to what I want. The 200 is a limitation, but I can work with it for now. Thanks! ...
written 11 days ago by oddjobs0
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Find all NCBI taxids in some group (e.g., all coronaviruses)
... I am trying to get the list of taxids of all coronaviruses which I plan to use in a script. Equivalently, the taxids of all viruses related to SARS-CoV is also a good starting point. However, I do not know how to extract this information efficiently. I can find the following links with NCBI, howeve ...
ncbi taxonomy browser sars rna written 11 days ago by oddjobs0 • updated 11 days ago by Joe17k
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Comment: C: (EDITED) Aligning complete viral RNAs
... Right. I am trying to align a finished sequence for a virus to the virus' reference sequence. So most mismatches/indels are just from viral mutations. I am not looking to do a multiple sequence alignment at this point. ...
written 4 weeks ago by oddjobs0
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Comment: C: Getting around wrong taxids in NCBI virus database
... Seems I made a rookie error! Thanks for the correction. I will look into both LASTZ and Nextstrain. I am not sure minimap2 is suitable, since it is designed for sequencing reads with high error-rate (especially indel error rates) rather than finished assemblies. I believe for it to perfectly work, ...
written 4 weeks ago by oddjobs0
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Comment: C: Getting around wrong taxids in NCBI virus database
... I see. Thanks for this information! So I will essentially need to get the taxid of the leaf nodes in this tree to ensure it is purely from one species. ...
written 4 weeks ago by oddjobs0
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(EDITED) Aligning complete viral RNAs
... It seems there may be potential mislabeling of the taxid of some sequences deposited in the NCBI virus database. For example, when I use taxid:694009 (SARS-CoV) to search for sequences, I see results reported for SARS-CoV2 as well (e.g., NC_045512). SARS-CoV2 has a taxid of 2697049. I wonder whethe ...
refseq skbio stripedsmithwaterman alignment written 4 weeks ago by oddjobs0
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Comment: C: No concern of human mRNA contamination in viral qPCR tests?
... Thanks for the response. My question arises because the protocol doesn't indicate any tests against the human transcriptome, while it presents tests against coronaviruses. They also compare the primer targets to other coronavirues through alignment and the results are shown in the protocol paper. I ...
written 11 weeks ago by oddjobs0
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(Closed) No concern of human mRNA contamination in viral qPCR tests?
... I have no experience in conducting PCR or qPCR. I am trying to understand some basic information about qPCR testing for SARS-CoV-2, and hence was reading through a typical protocol https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf. In the protocol it is mentioned that specifici ...
rt-pcr covid-19 sars-cov-2 testing qpcr pcr written 11 weeks ago by oddjobs0

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