Moderator: Michael Dondrup
Michael Dondrup ♦ 46k
- Reputation:
- 46,340
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- 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
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... 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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
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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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
0
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... `-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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
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... 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 Dondrup ♦ 46k
Latest awards to Michael Dondrup
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For A: Rna-Seq Data Analysis & Good Review/Research Article On Same
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For What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
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12 days ago,
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For A: Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics
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16 days ago,
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8 weeks ago,
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