[BioC] bsseq and BSmooth with RRBS
Alex Gutteridge
alexg at ruggedtextile.com
Thu Feb 21 17:31:08 CET 2013
I'm looking over the documentation for bsseq:
http://www.bioconductor.org/packages/2.11/bioc/html/bsseq.html
And the associated Genome Biology paper:
http://genomebiology.com/content/pdf/gb-2012-13-10-r83.pdf
From what I can see the method should work on reduced representation
bisulfite sequencing (RRBSeq) datasets as well as WGBSeq, though the
documentation only mentions WGBSeq. The only issue I can see being the
smoothing procedure which I thought might struggle in regions with
scattered CpGs in the RRBSeq.
I will have data in hand shortly to test this myself, but was just
curious if anyone on the list had run bsseq (successfully or otherwise)
on RRBS data before?
--
Alex Gutteridge
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