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kdkorthauer / dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
MIT License
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MeDipSeq #32

Closed dktanwar closed 4 years ago

dktanwar commented 4 years ago

Hi @kdkorthauer

Is it possible to use dmrseq with MeDiP-Seq data?

If so, what would be the parameters to be considered?

kdkorthauer commented 4 years ago

Hi @dktanwar,

Thank you for the question. dmrseq was designed for bisulfite sequencing data, where we obtain basepair-level signal. Unfortunately, MeDIP sequencing provides peak-level signal, so it requires a different modeling approach. One idea could be to convert the MeDIP data into a rough basepair-level signal based on all reads aligning each site and then model with methods for bisulfite sequencing data, but this is not a direction I have explored.

You may want to check out the MEDIPS Bioconductor package for working with your data.

Best, Keegan