Moderator: iw9oel_ad

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Posts by iw9oel_ad

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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 8.1 years ago by iw9oel_ad6.0k
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Comment: C: Bwa Option That Stops After N Minutes
... Okay, tests added... ...
written 8.1 years ago by iw9oel_ad6.0k
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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 8.1 years ago by iw9oel_ad6.0k
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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 8.1 years ago by iw9oel_ad6.0k
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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 8.1 years ago by iw9oel_ad6.0k
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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 8.1 years ago by iw9oel_ad6.0k
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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 8.2 years ago by iw9oel_ad6.0k
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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 8.3 years ago by iw9oel_ad6.0k
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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 8.3 years ago by iw9oel_ad6.0k
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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 8.3 years ago by iw9oel_ad6.0k

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