about cn.MOPS: paired vs unpaired
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Bogdan ▴ 620
@bogdan-2367
Last seen 22 days ago
Palo Alto, CA, USA

Dear all, 

a simple question about cn.MOPS function : 

getReadCountsFromBAM(BAMFiles, sampleNames, refSeqName, WL, mode, parallel = 0)

Here "mode" is described in the following way :  "Possible values are "paired" and "unpaired", whether the mapping algorithm was using a "paired" or "unpaired" strategy.". 

The question is : "paired" and "unpaired" refer to "paired-end reads" vs "single-end reads" ? 

And : what is necessary in order to parallelize the execution of the code ? Thank you ;) !

 

-- bogdan 

 

 

 

 

cn.mops • 618 views
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It seems so, considering the results of the function testPairedEndBam() from Rsamtools.

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@gunter-klambauer-5426
Last seen 8 months ago
Austria
Hello Bogdan, Thanks for using cn.mops. Yes, this refers to "paired-end reads" or "single-end reads"! Parallelization is implemented, you can simply set the parameter "parallel=4" of "getReadCountsFromBAM" or "cn.mops" and the code will be executed on 4 cores. The only thing that is necessary from the software-side is that the library "parallel" is installed. Regards, Günter On 2016-11-09 20:14, Bogdan Tanasa [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User Bogdan Tanasa <https: support.bioconductor.org="" u="" 2367=""/> wrote > Question: about cn.MOPS: paired vs unpaired > <https: support.bioconductor.org="" p="" 89254=""/>: > > Dear all, > > a simple question about cn.MOPS function : > > getReadCountsFromBAM(BAMFiles, sampleNames, refSeqName, WL, > mode, parallel = 0) > > Here "mode" is described in the following way : "Possible values are > "paired" and "unpaired", whether the mapping algorithm was using a > "paired" or "unpaired" strategy.". > > The question is : "paired" and "unpaired" refer to "paired-end reads" > vs "single-end reads" ? > > And : what is necessary in order to parallelize the execution of the > code ? Thank you ;) ! > > -- bogdan > > ------------------------------------------------------------------------ > > Post tags: cn.mops > > You may reply via email or visit > about cn.MOPS: paired vs unpaired > -- Günter Klambauer, PhD Institute of Bioinformatics Johannes Kepler University, Linz, Austria http://www.bioinf.jku.at/people/klambauer/
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