How to find differentially methylated regions from bigwig/wig/bedgraph files?
I have bisulfite sequencing data that has been aligned to the mm10 mouse genome, and the output that has been provided to me is in a bigwig file format. I know I can convert this filetype back to wig and bedgraph - which R/bioconductor package will allow me to identify differentially methylated regions using these file types?
1 answer
How are you planning on identifying differentially methylated regions?
With a wig format, you would only be able to detect differences in signal strength. The primary sequence information will be lost.
If you're planning on using actual sequence differences, you will need the original SAM/BAM alignments.
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