I have RRBS data which I have aligned to hg38 reference genome. CpG island annotation available with the package is only for hg18 assembly (cpgi.hg18.bed.txt). So, is liftOver an only option or the team has hg38 version hosted somewhere that I could download?

Same situation for refseq.hg18.bed.txt.

It would be a great favor if I can get these files for further analysis. Also, a process to generate these from either NCBI or from assembly goldenpaths like this.

Thanks a lot,

Satya

I wouldn't use liftOver, as you will likely get fragmentation of the islands (possibly across different chromosomes). It's simple enough to go to UCSC and download the data from them. Or you could use rtracklayer to get the data, but the direct table browser route is often simpler.