Moderator: Michael Dondrup
Michael Dondrup ♦ 45k
- 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 Dondrup ♦ 45k
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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 Dondrup ♦ 45k
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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 Dondrup ♦ 45k
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... 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 Dondrup ♦ 45k
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... 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 Dondrup ♦ 45k
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... [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 ...
written 6 days ago by
Michael Dondrup ♦ 45k
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... 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 Dondrup ♦ 45k
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... 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 Dondrup ♦ 45k
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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 Dondrup ♦ 45k
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... 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 Dondrup ♦ 45k
Latest awards to Michael Dondrup
Scholar
10 days ago,
created an answer that has been accepted.
For A: Sequence Blast Against Rfam Database
Appreciated
19 days ago,
created a post with more than 5 votes.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Popular Question
21 days ago,
created a question with more than 1,000 views.
For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
Appreciated
21 days ago,
created a post with more than 5 votes.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Popular Question
25 days ago,
created a question with more than 1,000 views.
For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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
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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?
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10 weeks ago,
created a question with more than 1,000 views.
For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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?
Appreciated
3 months ago,
created a post with more than 5 votes.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
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?
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For C: How To Generate Blast Database
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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?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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))
Appreciated
3 months ago,
created a post with more than 5 votes.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
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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