Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
45,430
Status:
Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
2 hours ago
Joined:
9 years 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: subset function limitation in R
... Hi, I agree with the question being closed, as it stands now. But the core problem is about not being specific enough to help, and that caused your question to become a generic question. There is no mention of gene names, only 'names', no specification of the data type, just 'mybigdata' (now it's T ...
written 4 days ago by Michael Dondrup45k
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Answer: A: Having trouble using wildcard
... Your search patter doesn't match the file names. in1=./temp_expt/Sample_MBM1${i}/MBM1${i}_R1_001.fastq \ in2=./temp_expt/Sample_MBM1${i}/MBM1${i}_R2_001.fastq \ while your file names look like MBM118-TTACGTGC-CAAGGTCT_S66_L008_R1_001.fastq If you are sure there is only on pair o ...
written 5 days ago by Michael Dondrup45k
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Comment: C: What can we learn from parasites?
... Hi Istvan, I think "what can we learn from parasites" really is the best way of saying it, "In praise of parasites" would be another if it hadn't been taken already. Thanks for your suggestion. ...
written 5 days ago by Michael Dondrup45k
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Comment: C: Are parasites good as model organisms?
... How about this? Are parasites good as model organisms? I am honestly not so much invested in the biostars post title, it sounded catchy to me. This page seems to describe nicely what I wanted to say "In praise of parasites": https://www.smithsonianmag.com/science-nature/praise-parasites-180971139/ ...
written 6 days ago by Michael Dondrup45k
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Comment: C: Are parasites finally good for something?
... Hi genomax, what I meant was that they help us understand some biological process and as a contrast to most people viewing them as a problem. In fact, I think they could be a good model for heme trafficking. With respect to any benefit to the fish, we haven't seen a lot of evidence for this yet, but ...
written 6 days ago by Michael Dondrup45k
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News: Beyond pest control: What can we learn from parasites?
... [Parasites][1] are infamous for exploiting other organisms for food, they are often treated as pests and pathogens with the narrow focus to get rid of them. Sea lice are no exception as major blood-feeding ectoparasites of farmed and wild fish. But can parasites help us to understand basic physiolog ...
in silico news parasitism heme docking written 6 days ago by Michael Dondrup45k
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Comment: C: How to extract a entire row based on a single key word from a csv or excel file?
... I thought that will also work with the pipe to head -1. Sorry, no ;) better to simply use `grep -m 1` to stop reading after the first match. ...
written 7 days ago by Michael Dondrup45k
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Comment: C: How to extract a entire row based on a single key word from a csv or excel file?
... Hi, sounds like Unix grep would be just as fine. Also, this is not bioinformatics, is it? Try: `grep -e "keyword" | head -1` ...
written 7 days ago by Michael Dondrup45k
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Comment: C: Newick trees analysis software
... Thank you, and thank you to jrj.healey for making a working script. I am not a python guy so I couldn't have done it. ...
written 9 days ago by Michael Dondrup45k
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Comment: C: RepeatModeler cannot be run in parallel
... You were indeed right with your assumption. Op did not use the latest version. When using version 1.0.8, the following is shown: -pa # Specify the number of shared-memory processors available to this program. RepeatModeler will use the processors to run BLAST searches ...
written 11 days ago by Michael Dondrup45k

Latest awards to Michael Dondrup

Scholar 10 days ago, created an answer that has been accepted. For A: Sequence Blast Against Rfam Database
Epic Question 4 weeks ago, created a question with more than 10,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Run Tmhmm In Interproscan 5 Standalone Version
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How To Run Tmhmm In Interproscan 5 Standalone Version
Scholar 7 weeks ago, created an answer that has been accepted. For A: Sequence Blast Against Rfam Database
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Do Bad Questions Even Exist?
Scholar 12 weeks ago, created an answer that has been accepted. For A: How do I find the set of a genomicrange? (same as union(gr, gr))
Scholar 3 months ago, created an answer that has been accepted. For A: How do I find the set of a genomicrange? (same as union(gr, gr))
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads From Bam That Overlap With Specific Regions?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Extract Reads From Bam That Overlap With Specific Regions?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How To Generate Blast Database
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads From Bam That Overlap With Specific Regions?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Plotting Exons Of A Transcript Using Bioconductor Genomegraphs
Scholar 3 months ago, created an answer that has been accepted. For A: How do I find the set of a genomicrange? (same as union(gr, gr))
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Plotting Exons Of A Transcript Using Bioconductor Genomegraphs
Scholar 3 months ago, created an answer that has been accepted. For A: How to start a website with jbrowse to show sequencing data?

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