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? 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]]

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

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 > > > [[alternative HTML version deleted]] ------------------------------ -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it Info: http://publicationslist.org/raffaele.calogero