Question: bsmooth and bsseq for RRBS
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5.4 years ago by
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Guest User12k wrote:
Hello, I am wondering whether one could use bsseq (and bsmooth-align) for RRBS data. Thanks a lot. -- output of sessionInfo(): none -- Sent via the guest posting facility at bioconductor.org.
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ADD COMMENTlink modified 5.4 years ago by Tim Triche4.2k • written 5.4 years ago by Guest User12k
Answer: bsmooth and bsseq for RRBS
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5.4 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
Just for reference, I have had good results using QuasR for RRBS, although there are certainly many other options, and I prefer to look at WGBS, given the choice. BiSeq is another RRBS-centric package you might investigate. For WGBS, Brent Pedersen has written the very cool bwa-meth: https://github.com/brentp/bwa-meth/ I'm horribly biased since colleagues of mine wrote some of the key components, but the overall pipeline is pretty slick if you start looking at WGBS data, either for comparison with RRBS or on its own. bsseq (the package) is very handy for making sense of the data; I haven't used BiSeq enough to say if it's categorically superior for RRBS, but it does use many of the same data structures (e.g. a SummarizedExperiment-based class to hold the read counts and coverage) so I imagine it would be easy to go back and forth for plotting purposes (which is where bsseq is particularly handy). JMHO --t On Wed, Jan 22, 2014 at 2:12 AM, Gilgi [guest] <guest@bioconductor.org>wrote: > > Hello, > > I am wondering whether one could use bsseq (and bsmooth-align) for RRBS > data. > > Thanks a lot. > > -- output of sessionInfo(): > > none > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.4 years ago by Tim Triche4.2k
Thanks a lot! From: Tim Triche, Jr. [mailto:tim.triche@gmail.com] Sent: Wednesday, January 22, 2014 7:14 PM To: Gilgi [guest] Cc: bioconductor@r-project.org; Gilgi Friedlander; bsseq Maintainer Subject: Re: [BioC] bsmooth and bsseq for RRBS Just for reference, I have had good results using QuasR for RRBS, although there are certainly many other options, and I prefer to look at WGBS, given the choice. BiSeq is another RRBS-centric package you might investigate. For WGBS, Brent Pedersen has written the very cool bwa-meth: https://github.com/brentp/bwa-meth/ I'm horribly biased since colleagues of mine wrote some of the key components, but the overall pipeline is pretty slick if you start looking at WGBS data, either for comparison with RRBS or on its own. bsseq (the package) is very handy for making sense of the data; I haven't used BiSeq enough to say if it's categorically superior for RRBS, but it does use many of the same data structures (e.g. a SummarizedExperiment-based class to hold the read counts and coverage) so I imagine it would be easy to go back and forth for plotting purposes (which is where bsseq is particularly handy). JMHO --t On Wed, Jan 22, 2014 at 2:12 AM, Gilgi [guest] <guest@bioconductor.org<mailto:guest@bioconductor.org>> wrote: Hello, I am wondering whether one could use bsseq (and bsmooth-align) for RRBS data. Thanks a lot. -- output of sessionInfo(): none -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 5.4 years ago by Gilgi Friedlander90
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