Moderator: Michael Dondrup
Michael Dondrup ♦ 44k
- Reputation:
- 44,200
- Status:
- Trusted
- Location:
- Bergen, Norway
- Website:
- https://licebase.org/
- Last seen:
- an hour ago
- Joined:
- 8 years, 6 months 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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... Hi, I don't exactly know what `1 != corrected_run` this is supposed to protect against, but from the name of the function, could it be that some bam files are paired and others not? Could the files that do not work have been truncated in some way: check out https://www.biostars.org/p/247903/ also i ...
written 12 hours ago by
Michael Dondrup ♦ 44k
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... Hello Ensembl Helen!
Looks like this just got bumped, or is it November 2018? Possibly such post should just be deleted to avoid confusion?
It might be advisable to include the full date and year in the post.
Please let us know if this assumption is correct.
Cheers!
...
written 3 days ago by
Michael Dondrup ♦ 44k
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... This question doesn't make much sense to me unless it is prone to trivial answers, please elaborate on available data, analysis, and what you have tried. ...
written 3 days ago by
Michael Dondrup ♦ 44k
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Comment:
C: cloning and vector design
... Hello The Bright Star!
We believe that this post does not fit the main topic of this site.
Not a bioinformatics question, no clarification was given.
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 dis ...
written 3 days ago by
Michael Dondrup ♦ 44k
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... This is a very general question, in particular what is bioinformatics web development? It really depends on the application case and requirements, and certainly the type of data to store. Note: Database Management Systems (DBMS) are a **back-end technology** meaning they are used for storing and ret ...
written 3 days ago by
Michael Dondrup ♦ 44k
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Comment:
C: Illegal Division by zero
... Ok, so this is not your code? In this case (aside from flaming the author), just to get a minimal quick fix, just replace line 179 in the original script:
- $features[$x] /= $features[$oligos+1];
+ $features[$x] = ($features[$oligos+1] > 0)? $features[$x] / $features[$oligos+1] : 'NA'; ...
written 3 days ago by
Michael Dondrup ♦ 44k
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Answer:
A: Illegal Division by zero
... You are trying to keep the total sum of all occurrences in `$features[$oligos+1]` (accessing the n+1th element ) with $oligos being some integer, a global variable from out of nowhere.
Note: this part of the array `@features` has never been initialized as 0. It works anyway in perl, because ($unde ...
written 4 days ago by
Michael Dondrup ♦ 44k
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... > how can I use rtracklayer and liftover function to liftover from
> Macaca Fascicularis genome to hg_19?
Even though this file exists, may I question to which extent it makes sense to lift-over between two different primate species? This certainly depends on your study and the scientific que ...
written 6 days ago by
Michael Dondrup ♦ 44k
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... It looks as if you are running code that you cannot fully understand. The last command gives you the difference between original snp set and hg19 snap set. Like the ones that couldn’t be converted. ...
written 7 days ago by
Michael Dondrup ♦ 44k
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... Assuming that you downloaded the chain file, you have to specify the right path. The path is empty because it’s not found where system.file expects it. ...
written 7 days ago by
Michael Dondrup ♦ 44k
Latest awards to Michael Dondrup
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2 days ago,
created an answer with at least 3 up-votes.
For A: Filter Polya/T And Other Repeats In Illumina Reads
Good Answer
3 days ago,
created an answer that was upvoted at least 5 times.
For A: What Does Bwa'S '-N' Parameter Mean?
Appreciated
3 days ago,
created a post with more than 5 votes.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher
3 days ago,
created an answer with at least 3 up-votes.
For A: Filter Polya/T And Other Repeats In Illumina Reads
Commentator
3 days ago,
created a comment with at least 3 up-votes.
For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
Popular Question
4 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
Teacher
11 days ago,
created an answer with at least 3 up-votes.
For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Appreciated
23 days ago,
created a post with more than 5 votes.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Popular Question
4 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
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
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4 weeks ago,
created an answer that has been accepted.
For A: How To Deal With Duplicate Row Names Error In R
Popular Question
6 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
Popular Question
7 weeks ago,
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For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
Popular Question
8 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
Good Answer
11 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: Extracting Sub-cellular location from Uniprot into tabular format
Popular Question
3 months ago,
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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: What Does Bwa'S '-N' Parameter Mean?
Scholar
3 months ago,
created an answer that has been accepted.
For A: How To Deal With Duplicate Row Names Error In R
Scholar
3 months ago,
created an answer that has been accepted.
For A: How To Deal With Duplicate Row Names Error In R
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: What Does Bwa'S '-N' Parameter Mean?
Popular Question
4 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
Scholar
4 months ago,
created an answer that has been accepted.
For A: Filling expr matrix for igraph
Great Question
4 months ago,
created a question with more than 5,000 views.
For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How Do I Access And Query Entire Genome Sequences With R
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