[BioC] How to handle data from solid SOLiD

rcaloger raffaele.calogero at gmail.com
Sun Nov 15 10:16:47 CET 2009


Dear Sunny,
I am working on SOLiD data.
I suggest to you to perform the primary mapping using an efficient mapping tool like PerM, Chen Y, Souaiaia T, Chen T.Bioinformatics 2009 Oct 1;25(19):2514-21.
Subsequently, you extract the genome location for each mapped read, and I insert them in a GenomeDataList.
At this point you can apply this data structure to conventional Bioconductor tools like as chipseq package.
I hope it help
Cheers
Raffaele

>Dear Martin,
>How to I know that people are already working on it?

>Sorry, I googled a lot to find any such information, but I could not find
>any  :-( 

>Thanks,
>S.


On Fri, Nov 13, 2009 at 4:33 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:


> > Sunny Srivastava wrote:
>   
>> > > Dear Bioconductor Helpers,
>> > > I have used Bioconductor for microarray data analysis.
>> > >
>> > > Can any one pls tell me if there are ways to handle data from SOLiD?
>>     
> >
> > Hi Sunny -- The software currently available in Bioconductor does not
> > handle SOLiD colorspace. Perhaps others in the Bioconductor community
> > are working on this? There is a rich collection of Bioconductor software
> > for handling sequence data in nucleotide space.
> >
> > Martin
> >
>   
>> > >
>> > > I have googled and found that a few packages mention support for SOLiD
>>     
> > but
>   
>> > > most of the examples are directed towards Solexa.
>> > >
>> > > Any help is greatly appreciated!
>> > >
>> > > Thanks,
>> > > S.
>> > >
>> > >       [[alternative HTML version deleted]]
>> > >
>> > > _______________________________________________
>> > > Bioconductor mailing list
>> > > Bioconductor at stat.math.ethz.ch
>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > > Search the archives:
>>     
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
> > --
> > Martin Morgan
> > Computational Biology / Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
> >
> > Location: Arnold Building M1 B861
> > Phone: (206) 667-2793
> >
>   

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-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
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