Moderator: Lars Juhl Jensen
Lars Juhl Jensen ♦ 11k
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- Copenhagen, Denmark
- Website:
- http://larsjuhljensen....
- Twitter:
- larsjuhljensen
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- Last seen:
- 3 years, 9 months ago
- Joined:
- 10 years, 7 months ago
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Posts by Lars Juhl Jensen
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... I partially agree, but only partially. I do think that there are some golden rules, which were summarized very well by lh3 and Pierre. However, as any golden rule, they cannot be applied in every case. Regarding I/O being a bottleneck, I have only ever experienced that when someone was doing somethi ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... Sorry if I offended you, but your comments really rubbed me the wrong way. You came across as being deeply sarcastic of what everyone else had recommended. I felt someone needed to point this out.
Numerous bioinformatics processes required in analysis of large datasets, e.g. sequencing data, requir ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... I'm afraid I fail to understand your humor. Your 10 rules are clearly sarcastic; however, if interpreted as such, you say that one should not stream and and not parallelize, despite that being precisely the way to efficiently process really big datasets. I'm sorry to have to say this, but I simply d ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... Others already said some of the key things:
- Calculate on streams instead of loading everything into memory. Pipes are great for that, but far from the only strategy.
- Perform independent calculations on different parts of the data in parallel. That way you can utilize compute clusters efficien ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... According to the documentation on the second page that you link to yourself, the behavior depends on the `-strand` argument:
-strand <+|-|both> (Count tags on specific strands relative to peak, default: both) ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... This one should probably be changed to be a forum post rather than a question. ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... If you are looking for the same sequence of, e.g., at least length 10 that is perfectly repeated at least 3 times with no spacer, you can do that with a regular expression:
(.{10,})\1\1
All you have to do is write a simple script in a language of your choice that searches for matches to this r ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... You will probably have more luck asking at [SEQanswers][1] than here, since this forum is purely about bioinformatics.
[1]: http://seqanswers.com/ ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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... You're very welcome, but Fisher's exact test will only get you the first step. Don't forget correction for multiple testing. ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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Comment:
C: Big Data tools for Bioinformatics
... Given how ill defined it is what constitutes "big data" and thus "big data tools", I don't think there is a good answer to this. Are NGS data big data? Are bioinformatics tools for analysis of NGS big data tools? Is R a big data tool? Are NoSQL databases big data tools? ...
written 3.8 years ago by
Lars Juhl Jensen ♦ 11k
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For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
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For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
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For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
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For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
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For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
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For A: Cog Paralogous And Orthologous Classes
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