[BioC] Minimal input data format for bsseq

[Aryee, Martin,Ph.D.]

Hi Kasper,

I'd like to use bsseq on a partially preprocessed whole genome bisulfite sequencing dataset. I have a data table with one row per CpG and columns for:

1. chromosome
2. position
3. number of reads supporting an unmethylated CpG (U)
3. number of reads supporting a methylated CpG (M)

Is it possible to turn this into an acceptable input for bsseq (perhaps with reduced functionality), or is it essential to run the BSmooth alignment suite to generate the complete set of columns typically used by bsseq?

Thanks,
Martin




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