[BioC] RRBS question
alexg at ruggedtextile.com
Wed Jan 22 11:15:46 CET 2014
On 21.01.2014 20:48, Gilgi Friedlander wrote:
> Hi Alex,
> Sorry to bother you, but I have a question regarding RRBS analysis.
> I saw your post from last year, and also was wondering if bsmooth can
> work well for RRBS data, as going to work on such data.
> I wanted to reply to the post on the mailing list, but didn't see
> such an option.
> If you already have results, and can share your experience if one can
> use bsmooth for RRBS, it will be great. And if not, if you have
> recommendations for other tools.
> Thanks a lot,
cc'ing the list for future reference and in case anyone else has
additional insights on RRBS analysis with Bioconductor:
I had mixed results with bsmooth and rrbs data when I tried it.
Certainly the various smoothing parameters required tweaking before it
would run successfully. I can let you know what worked for me, but I'd
be lying if I said I arrived at them through careful experimentation.
One also has to be cautious I think about the overall approach of
whether smoothing makes sense when the data from rrbs is by definition
non-contiguous. That said, bsmooth did run and did detect differential
methylated regions for us which looked correct on deeper inspection.
What bsmooth (by design I guess) does not detect are the single CpGs
that seem to change between experimental groups, but sit within larger
regions that clearly do not change. It's still an open question (in my
mind at least) whether such sites are likely to be biologically
significant or not.
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