Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
40,560
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Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
7 minutes ago
Joined:
7 years, 1 month ago
Email:
m*******@gmail.com

 

PhD in bioinformatics. Currently Researcher at the Sea Lice Research Centre, responsible for LiceBase, an infrastructure for genomic resources of sea lice, and analysis of genomics data from emerging genomes.

Posts by Michael Dondrup

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Comment: C: Download NCBI genomes using taxonomy id (taxid)
... To search by Taxid instead of name, change the following line: GENOME=$(esearch -db genome -query "$TAX"[orgn] | with: GENOME=$(esearch -db genome -query txid${TAX}[Organism:exp] | then you can run it like: `./fetchGenomeByTaxiID 59754` ...
written 3 minutes ago by Michael Dondrup41k
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Comment: C: Download NCBI genomes using taxonomy id (taxid)
... Sorry, wasn't ready editing. If you need a script that can download all draft assemblies of a certain taxon, e.g. all Arthropods instead, I have that too. ...
written 4 hours ago by Michael Dondrup41k
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Answer: A: Download NCBI genomes using taxonomy id (taxid)
... So here is a shell script I have used, that you could adapt for your needs. In the current form it downloads genome sequence and protein sequences, makes a blast database out of them, then joins all blastdbs in the directory into one alias db, called "SelectedArthropods". It works - mostly - an ...
written 4 hours ago by Michael Dondrup41k
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Comment: C: R: Error In Scan ... Line 7 Did Not Have 3 Elements
... Hello silkeverhelle! We believe that this post does not fit the main topic of this site. No longer relevant. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below ...
written 10 hours ago by Michael Dondrup41k
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Comment: C: How to do Genome Annotation?
... Sorry, I do not understand your request. ...
written 1 day ago by Michael Dondrup41k
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Comment: C: Does these algorithms need to train to estimate genetic network?
... Hello someone! We believe that this post does not fit the main topic of this site. It is unclear what you are asking, what have you tried? For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree pleas ...
written 2 days ago by Michael Dondrup41k
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Answer: A: sam file error
... It is unclear which command and version you are using, but most likely nohup is the culprit. If running under nohup, it is mandatory in newer versions of samtools (htslib) to specify the output file using option '-o sorted.bam', see the documentation http://www.htslib.org/doc/samtools.html ...
written 6 days ago by Michael Dondrup41k
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Comment: C: Southbridge overheating Problem
... Hello walkerzed1! We believe that this post does not fit the main topic of this site. Despite the name this is not a Biostar (Motherboard) support forum. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you ...
written 7 days ago by Michael Dondrup41k
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Comment: C: Calculate Free energy at 3'end of miRNA and 5'end or miRNA
... What have you tried? ...
written 8 days ago by Michael Dondrup41k
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Comment: C: How to Install SGE (Sun Grid Engine) on macOS Sierra?
... I think that OGE/SGE is pretty much dead these days. But then I would question that you need it in the first place. Why do you need a cluster software for a single computer, it would be way oversized a solution. ...
written 9 days ago by Michael Dondrup41k

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