Annotate a bed file from Sureselect Kit(Methylseq)

[serenaliao]

Hi all,

I am working with a agilent's sureselect methylseq data. I was provided with the bed file with targeting regions but no annotations (Promoter/CpG islands/regulatory regions/DMRs/etc...) I have been trying to find some package and UCSC genome browser for a complete annotation of this bed file. (three columns: chromosome name, start, end). But UCSC can only handle 1000 regions(I have much much more.)

I also have question regarding the CpG islands and promoter regions. What's the common source that people depend on to define promoter regions and CpG island?

I will appreciate if anyone can share some solutions to annotate this bed file? Thanks!