Moderator: biobot 0.0.77.a.1099

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The product of a machine learning experiment gone awry.

Posts by biobot 0.0.77.a.1099

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Comment: C: Bwa Option That Stops After N Minutes
... Most of the work is done in sbcl (Steel Bank Common Lisp - http://www.sbcl.org). Slime is an environment that lets Emacs talk to external Lisps, including Common Lisps like sbcl and other Lisps like Clojure. ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Comment: C: Bwa Option That Stops After N Minutes
... Okay, tests added... ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Comment: C: Bwa Option That Stops After N Minutes
... What version of bwa are you using? On 0.6.1 the -s flag is "maximum seeding interval size". ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Comment: C: Bwa Option That Stops After N Minutes
... Good point. I tested this and bwa is sensible about the way it processes the queries; bsw2_aln is called approx every 10 Mb of queries (I used a Lisp process on the other end of the FIFO to send blocks of Fastq data interactively and observed the results). ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Answer: A: Bwa Option That Stops After N Minutes
... I would not try to interrupt BWA, but rather create a script to feed the sequences to BWA for n minutes: Create a Perl script that writes sequences to STDOUT for n minutes e.g. using Perl alarm as other answers have suggested. When you do this catch the signal or use some other way to ensure that t ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Answer: A: Plink - Non Human Data
... I wanted to know about Plink's support for different organisms too, but could not find the information in the documentation. Looking at the source code was quicker: grep -E 'define.+Chromosome' helper.cpp void defineHorseChromosomes() void defineSheepChromosomes() void defineRiceChromosomes() void ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Answer: A: Esoteric Programming Languages
... I've done a fair bit of work in Common Lisp, including a SAM implementation, a BAM file read-management application, a bio-sequence library and a lot of pipelines and bespoke RNA-seq analysis for the WTSI. I chose Common Lisp (specficially SBCL) because I get great language features and good speed. ...
written 9.0 years ago by biobot 0.0.77.a.10996.1k
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Answer: A: Agile Development Of Bioinformatic Projects
... One example is the Wellcome Trust Sanger Institute's sample tracking application Sequencescape. I know that this project was using scrum in its early stages. I don't know whether that is still true. ...
written 9.1 years ago by biobot 0.0.77.a.10996.1k
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Answer: A: Gatk Indel Realignment Dies In A Memory Explosion... Any Fixes?
... That particular OutOfMemoryError indicates that you have pinned the garbage collector, meaning that the JVM is spending almost all its time trying to free memory, while hardly recovering anything of what is on the heap. This suggests that you are working with barely enough RAM for your task. The err ...
written 9.2 years ago by biobot 0.0.77.a.10996.1k
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Answer: A: Determine Where Is My Oligo Probe In The Gene? In Exonic Region Or Interonic Reg
... Go to Ensembl, select Human and type your probe name into the general search box. This will immediately locate your probe. Click on the link to open the viewer at the probe location. Use 'Configure this page' (on the left) to activate the Agilent probe tracks. Zoom out a little to see the probe in t ...
written 9.2 years ago by biobot 0.0.77.a.10996.1k

Latest awards to biobot 0.0.77.a.1099

Scholar 5.1 years ago, created an answer that has been accepted. For A: R - Append Item Iteratively To Matrix?
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Bwa Option That Stops After N Minutes
Scholar 5.1 years ago, created an answer that has been accepted. For A: Exome Sequencing: Masking The Non-Genic Sequences ?
Appreciated 5.1 years ago, created a post with more than 5 votes. For A: Bwa Option That Stops After N Minutes
Scholar 5.1 years ago, created an answer that has been accepted. For A: R - Pairwise Combinations Of Rows From Table?
Scholar 5.1 years ago, created an answer that has been accepted. For A: Alignment Algorithm
Scholar 5.1 years ago, created an answer that has been accepted. For A: How To Filter Bam File
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: Huge Ngs Data Storage And Transferring
Scholar 5.1 years ago, created an answer that has been accepted. For A: Split Fastq File Into Different Files Only Comprising One Chromosome Each
Good Answer 5.1 years ago, created an answer that was upvoted at least 5 times. For A: A Universal Format For Expression Data?
Appreciated 5.7 years ago, created a post with more than 5 votes. For C: How To Find Out The Mismatchs Of An Alignment Entry In The Sam File?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Bwa Option That Stops After N Minutes
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Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Huge Ngs Data Storage And Transferring
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: A Universal Format For Expression Data?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Bed Files Comparison
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Tracking The Version Of Third Party Tools Used
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: How To Generate Mutations In Sequences Of A Fasta File?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Bwa Option That Stops After N Minutes
Appreciated 8.3 years ago, created a post with more than 5 votes. For C: How To Find Out The Mismatchs Of An Alignment Entry In The Sam File?

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