about cn.MOPS: paired vs unpaired
1
0
Entering edit mode
Bogdan ▴ 670
@bogdan-2367
Last seen 5 months 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 • 1.1k views
ADD COMMENT
0
Entering edit mode

It seems so, considering the results of the function testPairedEndBam() from Rsamtools.

ADD REPLY
0
Entering edit mode
@gunter-klambauer-5426
Last seen 3.2 years 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/
ADD COMMENT

Login before adding your answer.

Traffic: 579 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6