Moderator: Michael Dondrup

gravatar for Michael Dondrup
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Bergen, Norway
Website:
https://licebase.org/
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3 hours ago
Joined:
10 years, 11 months ago
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Posts by Michael Dondrup

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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Great! I have now scheduled a hands-on week in April (9.-15.) but am keeping it flexible. Hopefully, we can also contribute something this time, and if it is only thorough testing. ...
written 6 days ago by Michael Dondrup48k
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Hello and Happy New Year! After having used the CVGA book with very good results last year I would like to repeat using the book for a practical session again this spring semester. I particularly liked that one could hand out the document for self-study and hands on and afterwards the students pres ...
written 6 days ago by Michael Dondrup48k
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Comment: C: makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is no
... I think that is a different error. It is best to contact NLM support directly. ...
written 7 weeks ago by Michael Dondrup48k
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Comment: C: RepeatModeler : build_lmer_table failed. Exit code 256
... Is the tool build_lmer_table installed correctly? Can you run it and does it output something like the output below? Possibly the tool is running out of memory, how much RAM do you have? $build_lmer_table build_lmer_table Version 1.0.5 Usage: build_lmer_table -l -sequence ...
written 8 weeks ago by Michael Dondrup48k
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Comment: C: How should I begin to assemble my transcripts?
... You can still do that after installing software via bio/conda see https://conda.io/projects/conda/en/latest/ and https://bioconda.github.io/ for what it can do. Caveat: In principle, I do agree with genomax that a competent sysadmin should install software, and that is the best way for you to get ...
written 8 weeks ago by Michael Dondrup48k
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Comment: C: How should I begin to assemble my transcripts?
... could you install via conda/bioconda instead? That might be easier and pull the dependencies for you. ...
written 9 weeks ago by Michael Dondrup48k
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Comment: C: Downloading SRA data
... Did you follow the instructions here? https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit There is a quick test of fastq-dump. ...
written 9 weeks ago by Michael Dondrup48k
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Answer: A: How should I begin to assemble my transcripts?
... I think you are on the right track, running long running multi-parameter scripts directly from the commandline can be cumbersome and after a while you never know which command actually succeeded. A hint to make your life easier: make a simple shell script wrapper for the trinity call. That way, you ...
written 9 weeks ago by Michael Dondrup48k
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Comment: C: How can I convert genebank file to .gff file? I am using linux or any other pyth
... Please note that "this code" does not mean anything, and "from online" is not a place. please be more specific. If you are an absolute beginner it is advised that you learn the basics about the linux and the commandline first. We cannot teach you that here. ...
written 9 weeks ago by Michael Dondrup48k
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Answer: A: Pseudogenes in the human genome annotation
... You can use Ensembl BioMart with the following query: [very long BioMart query..... Modify parameters as you like][1] There are many sub-types of pseudo genes, the query outputs the gene type in the last column. [1]: http://www.ensembl.org/biomart/martview/d5e8623bf33a920fd3fdf6149c374e2a?VIR ...
written 10 weeks ago by Michael Dondrup48k

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Scholar 7 weeks ago, created an answer that has been accepted. For A: Heatmaps In R With Huge Data
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