Moderator: Lars Juhl Jensen

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Posts by Lars Juhl Jensen

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Comment: C: Good practices while dealing with very large datasets
... 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 4 months ago by Lars Juhl Jensen11k
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Comment: C: Good practices while dealing with very large datasets
... 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 4 months ago by Lars Juhl Jensen11k
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Comment: C: Good practices while dealing with very large datasets
... 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 4 months ago by Lars Juhl Jensen11k
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Answer: A: Good practices while dealing with very large datasets
... 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 4 months ago by Lars Juhl Jensen11k
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Answer: A: Strand information when doing peak annotation with HOMER
... 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 4 months ago by Lars Juhl Jensen11k
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Comment: C: What is the definition of "read depth" vs "coverage"? (again...)
... This one should probably be changed to be a forum post rather than a question. ...
written 4 months ago by Lars Juhl Jensen11k
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Answer: A: In search of best tool for finding repeats
... 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 4 months ago by Lars Juhl Jensen11k
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Comment: C: RiboZero kit -- can you do smaller reactions?
... You will probably have more luck asking at [SEQanswers][1] than here, since this forum is purely about bioinformatics. [1]: http://seqanswers.com/ ...
written 4 months ago by Lars Juhl Jensen11k
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Comment: C: PFAM, KEGG enrichment for non model organism
... You're very welcome, but Fisher's exact test will only get you the first step. Don't forget correction for multiple testing. ...
written 4 months ago by Lars Juhl Jensen11k
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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 4 months ago by Lars Juhl Jensen11k

Latest awards to Lars Juhl Jensen

Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Scholar 6 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Scholar 6 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
Scholar 8 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Scholar 8 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Scholar 8 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Scholar 9 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Cylon 9 months ago, received 1,000 up votes.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Scholar 9 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Scholar 9 months ago, created an answer that has been accepted. For A: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Cog Paralogous And Orthologous Classes

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