Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
46,340
Status:
Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
2 hours ago
Joined:
9 years, 8 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 • 5,057 results • page 1 of 506 • next >
1
vote
1
answer
81
views
1
answers
Comment: C: Scale cores down when close to memory limit snakemake/nextflow
... I think it will be better to implement some sort of fail-over management. Take the return value of a job, check for memory errors and re-start, possibly once the load is lower. ...
written 27 days ago by Michael Dondrup46k
0
votes
1
answer
81
views
1
answers
Answer: A: Scale cores down when close to memory limit snakemake/nextflow
... On Linux systems you could read /proc/meminfo, before starting processes and only start a new process if enough free mem is available, however, in general it is maybe best to leave memory management to the OS. $ cat /proc/meminfo MemTotal: 2113418852 kB MemFree: 122602 ...
written 27 days ago by Michael Dondrup46k
0
votes
0
answers
60
views
0
answers
Comment: C: genome sequencing ?
... 5. These are not a bioinformatics questions 6. Please show that you have taken some reasonable effort to solve your problem. (hint: use online search) ...
written 27 days ago by Michael Dondrup46k
0
votes
1
answer
135
views
1
answers
Comment: C: How can I select highly variable genes from the RNASeq gene dataset?
... For co-expression analysis, you might use MAD with a certain threshold (e.g. MAD > 2) but remember that such thresholds are necessarily arbitrary. ...
written 28 days ago by Michael Dondrup46k
1
vote
1
answer
135
views
1
answers
Answer: A: How can I select highly variable genes from the RNASeq gene dataset?
... There is no need to cite simple statistics such as variance or Z statistics, however, you might consider [median absolute deviation][1] (MAD) as a robust alternative to variance, afaik this is commonly used as a filtering step in network analysis. If you do the filtering in R or another software, yo ...
written 28 days ago by Michael Dondrup46k
0
votes
0
answers
26
views
0
answers
Comment: C: I NEED HELP..PLEASE ANY EXPERT OF DNA SP
... Hello rabiatabassumhki! We believe that this post does not fit the main topic of this site. Not a real 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 reply be ...
written 7 weeks ago by Michael Dondrup46k
0
votes
0
answers
26
views
0
answers
Comment: C: I NEED HELP..PLEASE ANY EXPERT OF DNA SP
... Hello rabiatabassumhki! We believe that this post does not fit the main topic of this site. It is unclear what you are asking 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 wh ...
written 7 weeks ago by Michael Dondrup46k
0
votes
1
answer
153
views
1
answers
Comment: C: Blastp not matching to reference more than 1000 entries.
... `-titile "test"` should be `-title "test"` Just in case you might have overlooked the error message, you didn't get your database rebuilt. ...
written 8 weeks ago by Michael Dondrup46k
4
votes
1
answer
153
views
1
answers
Answer: C: Blastp not matching to reference more than 1000 entries.
... ok, how long is the query effectively? And are you getting no hits at all or is the desired hit just not among them? In the first case try setting -evalue 10000 or so, in second case change -num_descriptions and -num_alignments to 10000 or so. ...
written 8 weeks ago by Michael Dondrup46k
1
vote
1
answer
153
views
1
answers
Comment: C: Blastp not matching to reference more than 1000 entries.
... What are the exact commands used for makeblastdb and blastp? If a sequence is present exactly, it should definitely be found with an e-value close to 0, unless it is too short, the db too big, the e-value cutoff is too conservative or something else went wrong (there are a quite a few different thin ...
written 8 weeks ago by Michael Dondrup46k

Latest awards to Michael Dondrup

Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For A: Rna-Seq Data Analysis & Good Review/Research Article On Same
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
Scholar 16 days ago, created an answer that has been accepted. For A: Comparative Microbial Genomics
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
Scholar 8 weeks ago, created an answer that has been accepted. For A: Comparative Microbial Genomics
Appreciated 8 weeks ago, created a post with more than 5 votes. For Conversion Of Blat Output To Sam/Bam
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
Student 12 weeks ago, asked a question with at least 3 up-votes. For Conversion Of Blat Output To Sam/Bam
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Comparative Microbial Genomics
Teacher 4 months 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 months ago, created a question with more than 5,000 views. For Efficient Fastq Parsing And Manipulation In Java (With Or Without Biojava)
Appreciated 5 months ago, created a post with more than 5 votes. For Should We Have A Biostar Conference Or Meeting?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Looking For Bioinformatics Job In Germany
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How Do I Access And Query Entire Genome Sequences With R
Appreciated 6 months ago, created a post with more than 5 votes. For What Is Your Experience With Gmod Tools Or Alternatives?
Appreciated 7 months ago, created a post with more than 5 votes. For Screen shots of text (please don't)!
Teacher 7 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 7 months ago, created an answer with at least 3 up-votes. For A: Looking For Bioinformatics Job In Germany

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2325 users visited in the last hour