Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
45,940
Status:
Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
3 days, 5 hours ago
Joined:
9 years, 4 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

<prev • 5,039 results • page 1 of 504 • next >
0
votes
2
answers
179
views
2
answers
Comment: C: Can DESeq2 used for DRIP-seq analysis and how?
... Hi, thanks for accepting this and I hope it helps. Given the sparsity of the information and also my lack of knowledge of the data type, I am not sure if the votes are justified yet. Please let us know how it turns out. ...
written 26 days ago by Michael Dondrup46k
1
vote
2
answers
179
views
2
answers
Comment: C: Can DESeq2 used for DRIP-seq analysis and how?
... Hi Friederike, first thanks a lot for the relevant hint. Maybe you would like to give an answer yourself. For explanation, the reason for not recommending DEseq was that I was unable to find any paper that has used this combination of tools in their Methods. Whenever the terms appeared in the same ...
written 26 days ago by Michael Dondrup46k
4
votes
2
answers
179
views
2
answers
Answer: A: Can DESeq2 used for DRIP-seq analysis and how?
... In short, afaik, DESeq2 cannot be used for differential peak expression analysis as required by DRIP seq. Longer answer: That doesn't mean that one could not somehow run DESeq(2) or other DE analysis packages on these data, e.g. after re-formatting, inserting 'pseudo'-transcript regions and counts ...
written 28 days ago by Michael Dondrup46k
0
votes
2
answers
179
views
2
answers
Comment: C: About DESeq2 analysis
... I have added a link to the DRIP seq wikipedia entry. It should be quite clear what the implications are. I have also changed the title to more specific. ...
written 28 days ago by Michael Dondrup46k
1
vote
1
answer
139
views
1
answers
Comment: C: How to extract from a large text file in R
... It is perfectly possible to read millions of lines in R using e.g. scan. I am guessing that the data contains SNP id's and that you want to extract a subset of rows from the larger file based on ids given in another file. I think we have multiple good solutions for this all over the place already, n ...
written 29 days ago by Michael Dondrup46k
0
votes
1
answer
158
views
1
answers
Comment: C: Need Help: How can I perform Emboss-sixpack on multi-sequences fasta file
... Why call awk from python? Anyway you have to adapt the quotes. E.g. escape them or use alternative quotes. Like qq in Perl. Don’t know if python has similar functionality Of course it has something similar... https://stackoverflow.com/questions/29559905/does-python-have-an-equivalent-of-perls-qq ...
written 4 weeks ago by Michael Dondrup46k
1
vote
0
answers
109
views
0
answers
Comment: C: kmer analysis for sequences of behavior
... Looks like a problem for a hidden Markov model. ...
written 4 weeks ago by Michael Dondrup46k
0
votes
1
answer
160
views
1
answers
Comment: C: blastn not returning all the expected results
... > We are looking at the complete genome of roughly 20 000 bacterial species and we expect to find the queried gene in most of them. That sounds like a contradiction. Please clarify ...
written 4 weeks ago by Michael Dondrup46k
1
vote
1
answer
160
views
1
answers
Answer: A: blastn not returning all the expected results
... You cannot use blastn for this purpose. Your nucleotide sequence is not well conserved. To find all possible orthologs you have to compare protein sequences. Use either translated protein seq with tblastn or tblastx with a nucleotide query or protein queries on a protein database from annotated prot ...
written 4 weeks ago by Michael Dondrup46k
1
vote
0
answers
150
views
0
answers
Comment: C: low bootstrap value?
... You could also try to create alignments for each protein first, and then concatenate the alignments after that. That might avoid artificial alignments across junctions. You could also try skip the gblocks trimming step, as it also might remove some phylogenetically important regions. ...
written 4 weeks ago by Michael Dondrup46k

Latest awards to Michael Dondrup

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Comparative Microbial Genomics
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Are There Internships In Bioinformatics? How Can A Foreign Student Get Started I
Great Question 5 weeks ago, created a question with more than 5,000 views. For Efficient Fastq Parsing And Manipulation In Java (With Or Without Biojava)
Appreciated 5 weeks ago, created a post with more than 5 votes. For Should We Have A Biostar Conference Or Meeting?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Looking For Bioinformatics Job In Germany
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How Do I Access And Query Entire Genome Sequences With R
Appreciated 11 weeks ago, created a post with more than 5 votes. For What Is Your Experience With Gmod Tools Or Alternatives?
Appreciated 3 months ago, created a post with more than 5 votes. For Screen shots of text (please don't)!
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How Do I Access And Query Entire Genome Sequences With R
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Looking For Bioinformatics Job In Germany
Scholar 4 months ago, created an answer that has been accepted. For A: Sequence Blast Against Rfam Database
Epic Question 5 months ago, created a question with more than 10,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Run Tmhmm In Interproscan 5 Standalone Version
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Run Tmhmm In Interproscan 5 Standalone Version
Scholar 6 months ago, created an answer that has been accepted. For A: Sequence Blast Against Rfam Database
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Do Bad Questions Even Exist?
Scholar 7 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))

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1619 users visited in the last hour