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.
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