User: Fabian Bull
Fabian Bull • 1.3k
- Reputation:
- 1,270
- Status:
- Trusted
- Location:
- German
- Website:
- http://mybioinformatic...
- Twitter:
- peri4n
- Last seen:
- 3 years, 6 months ago
- Joined:
- 7 years ago
- Email:
- b**********@googlemail.com
PhD student of bioinformatics.
Doing assemblys all day. :D
Interessted in programming languages. specially in scala.
Posts by Fabian Bull
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... In case you did not know already: You can import scala.collection.JavaConversions.asScalaIterator and you the SamLocusIterator as every iterator. e.g.: for( entry <- iterator) { do something meaningful with entry } Saves some LOC and looks much cleaner.
...
written 4.1 years ago by
Fabian Bull • 1.3k
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... Does anyone know how to specify the directory Allpaths-LG uses to store its temporary files?
I set TMPDIR and TMP_DIR but none of them works. I get hundreds of errors of type:
Failed to create temporary file from /tmp/tmp_process_name_Xo1BJPS: Permission denied [errno=13].
I have no root access s ...
written 5.3 years ago by
Fabian Bull • 1.3k
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... But if you writing data not conforming the specification, nothing can work well. The questions becomes: Which approach can be easier modified? And that would probably be 'handwritten'.
...
written 5.5 years ago by
Fabian Bull • 1.3k
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... If you know what you are doing, handwritten code is always faster. The questions are: Do we know what we are doing (most often we are no experts of the problem)? Is the performance gain worth the effort?
...
written 5.5 years ago by
Fabian Bull • 1.3k
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8 follow
6
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... Bioinformatics analysis often deals with parsing file formats (e.g. GFF, VCF). Unfortunately there are many parsers out there, that only implement a subset of the specification, perform bad on large files or only work on some datasets.
Because parsing is a very old and well understood problem in co ...
written 5.5 years ago by
Fabian Bull • 1.3k
• updated
5.5 years ago by
Hernán • 110
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... IMHO, the advantage of SGA is a desirable scaling behavior and not better assembly performance.
I have never compared assembler very detailed (my boss did it in his thesis). The only thing I can tell, CLC produces by far the best N50 values.
...
written 5.6 years ago by
Fabian Bull • 1.3k
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... More of a comment but an answer but I though it could help you anyway.
The amount of computational power you need depends on the sequencing depth you are going to use. There are assemblers which will need much more RAM than you have.
I remember reading in the LG-Allpaths manual, the time and RAM th ...
written 5.6 years ago by
Fabian Bull • 1.3k
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... Could you explain what you mean by CN? I assume copy number? CN2 are snps which occur in 2 variations? Sorry but I am not really into the snp terminology.
...
written 6.2 years ago by
Fabian Bull • 1.3k
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... They were sequenced and assembled separately. My idea was that maybe the duplicated regions collapse in the assembly and therefore are mapped twice as often as the other regions.
...
written 6.2 years ago by
Fabian Bull • 1.3k
11
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2.3k
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1
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... I am searching for hints of polyploidy in two species:
My hypothesis is that species A is diploid and B is tetraploid.
Because I have different sequencing depth in the 2 species I extracted
reads in the ration 1:20 ( ratio of the genome sizes) to get similar expected coverages.
These two sets of ...
written 6.2 years ago by
Fabian Bull • 1.3k
• updated
6.2 years ago by
Chris Miller ♦ 20k
Latest awards to Fabian Bull
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Contaminating Sequences And Genome Assembly
Popular Question
3.9 years ago,
created a question with more than 1,000 views.
For Contaminating Sequences And Genome Assembly
Popular Question
3.9 years ago,
created a question with more than 1,000 views.
For Detecting Polyploidy Using An Assembly
Teacher
3.9 years ago,
created an answer with at least 3 up-votes.
For A: What Is The N50 Contig Number (Not N50 Length)?
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For A: Linux Distros Best Suited For Bioinformatics?
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For A: Levenshtein Distance Vs Smith-Waterman Algorithm
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For A: How Would You Use Open Source Tools For Laboratory Notebook System ?
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For A: How Do You Generate/Obtain The Citation Block From A Given Paper?
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For Detecting Polyploidy Using An Assembly
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For Favorite Sequence Layout/Typesetting In Latex
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For Coverage Experiment To Indicate Polyploidy.
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For Your Bioinformatics 'Aha-Experience'
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For Esoteric Programming Languages
Good Question
4.6 years ago,
asked a question that was upvoted at least 5 times.
For Detecting Polyploidy Using An Assembly
Good Question
4.6 years ago,
asked a question that was upvoted at least 5 times.
For Coverage Experiment To Indicate Polyploidy.
Good Question
4.6 years ago,
asked a question that was upvoted at least 5 times.
For Your Bioinformatics 'Aha-Experience'
Good Question
4.6 years ago,
asked a question that was upvoted at least 5 times.
For Esoteric Programming Languages
Good Answer
4.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Linux Distros Best Suited For Bioinformatics?
Good Answer
4.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Levenshtein Distance Vs Smith-Waterman Algorithm
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Detecting Polyploidy Using An Assembly
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Favorite Sequence Layout/Typesetting In Latex
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Esoteric Programming Languages
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Experience With Parser Generators For Common Formats
Guru
4.6 years ago,
received more than 100 upvotes.
Centurion
4.6 years ago,
created 100 posts.
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