methods 2: smoothing DNAm levels within each sample (e.g. https://t.co/sEeNXJcvlL) helped with precision and reduced potential technical variation - shoutout to the `bsseq` Bioconductor package by @PeteHaitch and @KasperDHansen https://t.co/ukMl05IsuW 9/
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@aaronquinlan BSmooth (http://t.co/6Bl6PFoWNt) and Bismark (http://t.co/yb4nmUKUYb) are both options that work with Bowtie 1 & 2.
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From @rafalab: BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions http://t.co/kT6sA7Kh
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BSmooth: Bis-seq analysis pipeline from Kasper Hansen, Ben Langmead & Rafa Irizarry http://t.co/vWX0O8KN #bioinformatics #epigenomicsissue