Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
45,270
Status:
Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
40 minutes ago
Joined:
8 years, 11 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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Comment: C: loop several conditions R
... Not sure if that question really fits here, but for now your code is faulty: ngenes<-nrow(PGC_predix_1) PGC_predix_1 is undefined, or possibly defined elsewhere in your environment, maybe PGC_predix was meant. That is why you get the same output, the number of rows in this variable. It pr ...
written 3 days ago by Michael Dondrup45k
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Comment: C: Imagining Alien Biology
... Hi, there's a SE site for this: https://worldbuilding.stackexchange.com/ you could try there with a bit more concrete question. ...
written 3 days ago by Michael Dondrup45k
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Job: Postdoctoral position in Computational Biology and Gene Regulation, University of Oslo, Norway
... Applications are invited for a 3 year position as Postdoctoral Fellow in the Computational Biology and Gene Regulation Group at the Norwegian Centre for Molecular Medicine, University of Oslo, a Nordic EMBL partner for Molecular Medicine. The research group is lead by Anthony Mathelier (http://m ...
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Comment: C: RNA-Seq Differential Expression Bash Scripting Error
... Might be, or it could cause a consequential error. Please post the script as a text file (for easy copy paste for us to test). 141 is a SIGPIPE and I guess you have a superfluous pipe character in your call. ...
written 19 days ago by Michael Dondrup45k
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Comment: C: RNA-Seq Differential Expression Bash Scripting Error
... Hi, I agree that it would be better to post your script as text. Anyway, you seem to use environment modules from http://modules.sourceforge.net/ I haven't seen this done before for bioinformatics tools, but there might be a good reason to do it that way in your case, it is worth finding out the mot ...
written 19 days ago by Michael Dondrup45k
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Comment: C: Strange Error while running STAR.
... This might be related to your zcat options, they look funny, in particular zcat doesn't have -c switch, -c is used with gunzip to cause equal behavior as zcat. Try: --readFilesCommand "zcat" or --readFilesCommand "zcat -f" or --readFilesCommand "zcat -f --stdout" ...
written 4 weeks ago by Michael Dondrup45k
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Comment: C: Four protein structures
... Hello hisham.alhawal! We believe that this post does not fit the main topic of this site. 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, we'll be happy to ...
written 5 weeks ago by Michael Dondrup45k • updated 5 weeks ago by zx87546.2k
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Comment: C: FASTQ alignment result is really bad
... Neither am I, sorry, but maybe you can download an older version of bwa that supports colorspace. ...
written 5 weeks ago by Michael Dondrup45k
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Comment: C: FASTQ alignment result is really bad
... Oh, these could be colorspace data, they need to be analysed differently! Try option -c with bwa and see if that improves the alignment. See http://seqanswers.com/forums/showthread.php?t=16621 ...
written 5 weeks ago by Michael Dondrup45k
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Comment: C: FASTQ alignment result is really bad
... It is rare for current RNA-seq protocols to see failed sequence quality and N content. Check how the fastq extraction went well, just download and extract again using SRA toolkit. Then possibly you need to apply quality trimming or select a better dataset. ...
written 5 weeks ago by Michael Dondrup45k

Latest awards to Michael Dondrup

Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Do Bad Questions Even Exist?
Scholar 4 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 5 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))
Good Answer 5 weeks 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 5 weeks ago, created an answer with at least 3 up-votes. For A: How To Extract Reads From Bam That Overlap With Specific Regions?
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: How To Generate Blast Database
Good Answer 6 weeks 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 7 weeks ago, created an answer with at least 3 up-votes. For A: Plotting Exons Of A Transcript Using Bioconductor Genomegraphs
Scholar 7 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))
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Plotting Exons Of A Transcript Using Bioconductor Genomegraphs
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to start a website with jbrowse to show sequencing data?
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to start a website with jbrowse to show sequencing data?
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to start a website with jbrowse to show sequencing data?
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
Epic Question 10 weeks ago, created a question with more than 10,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Student 10 weeks ago, asked a question with at least 3 up-votes. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?

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