Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
42,280
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Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
59 minutes ago
Joined:
7 years, 5 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: Why does submitting high-throughput sequence data to GEO from an Amazon EC2 inst
... This might not really solve the problem but: Does geo have a way to get some hash like sha or md5? If the checksum is ok, I would not bother too much. I would just want to make sure the files are not truncated. ...
written 1 hour ago by Michael Dondrup42k
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Comment: C: Help in regard of sequencing data
... Yes, depends on what the requirements are and it is futile to speculate, however, at that level, I would also worry about computational resources. If the supervisors do not provide enough guidance on data selection, do they provide sufficient computational infrastructure? The setup of the pipeline m ...
written 1 hour ago by Michael Dondrup42k
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Comment: C: Help in regard of sequencing data
... If possibly, try to avoid working with human data because there are much more restrictions on use of human data than on model organism data, and most pipelines will work comparably more performant on smaller animal genomes. ...
written 1 hour ago by Michael Dondrup42k
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Comment: C: Help in regard of sequencing data
... Hello humaira.amin96! We believe that this post does not fit the main topic of this site. This question is far to broad, please invest in necessary preparations like doing an internet and literature search. For this reason we have closed your question. This allows us to keep the site focused on ...
written 1 hour ago by Michael Dondrup42k
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Comment: C: How to Create comparison venn diagram using SILVA,GREENGENES,RDP,NCBI and OTT da
... Venn diagrams are for depicting the sizes of intersections of sets, so you need to define what the intersection between the databases you have means and implement that first, to determine what you are going to depict. e.g. what does intersect(SILVA, NCBI) mean? Most likely this will involve some se ...
written 20 hours ago by Michael Dondrup42k
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Answer: A: blast query coverage using perl
... Surprising answer maybe, you cannot calculate the correct query coverage from tabular output of blast. Query coverage is **not** **equal** to: **abs(qend-qstart)/qlength**. While often weekly defined, I normally have seen query coverage as the proportion of sequence covered by the alignment. Why i ...
written 1 day ago by Michael Dondrup42k
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Answer: A: Tools to identify the non-coding RNAs
... There is no such tool that reliably identifies *all* non-protein coding RNA's de-novo, you need to use a chain of tools and then from my (limited) experience the predictions are pretty bad compared to protein-coding gene prediction for some. The most popular tools: - [RNAmmer][1] for ribosomal RNA ...
written 1 day ago by Michael Dondrup42k
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Comment: C: Bash call variables from one script to other
... Hello deepak.k.choubey! We believe that this post does not fit the main topic of this site. Not a bioinformatics question. 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 ...
written 2 days ago by Michael Dondrup42k
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Comment: C: Shiny app does not launch browser automatically
... No, shiny is not a bioinformatics package. ...
written 4 days ago by Michael Dondrup42k
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Comment: C: Shiny app does not launch browser automatically
... Hello zhang.jianhai! We believe that this post does not fit the main topic of this site. Not a bioinformatics question. 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 ...
written 5 days ago by Michael Dondrup42k

Latest awards to Michael Dondrup

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: I Am Preparing A Course On Ngs: Any Suggestion ?
Scholar 16 days ago, created an answer that has been accepted. For A: Can 167 contigs in my genome be stitched in to one fasta sequence
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: What Are Numbers Every Bioinformatician Should Know?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Genomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: R: Error In Scan ... Line 7 Did Not Have 3 Elements
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: R: Error In Scan ... Line 7 Did Not Have 3 Elements
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Scholar 12 weeks ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Great Question 3 months ago, created a question with more than 5,000 views. 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: Comparing Alignments In An Iterative Process With Perl
Scholar 3 months ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Scholar 3 months ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Comparing Alignments In An Iterative Process With Perl
Scholar 3 months ago, created an answer that has been accepted. For A: Protein Back Translation For Aneides Flavipunctatus
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Comparing Alignments In An Iterative Process With Perl
Scholar 3 months ago, created an answer that has been accepted. For A: mirDeep2 using bowtie vs. bwa - why do more aligned reads yield less miRNA
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Why Don'T We Use Binary Format?

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