Hi,
I'm interested in analyzing the methylation of the TRPV1 gene. I need to find CpG islands as well as CpG island shores, since I've read these these shores can also be differentially methylated, even when the CpG islands aren't.
Could anyone point me to some web based or desktop tools to find CpG island shores? Or, if there aren't any tools off-the-shelf, could you describe a method for finding these shore regions?
Thanks.
I tried to write a perl code to subtract 2000bp and add 2000 to the CpG island region to get CpG shore regions (55436 CpG shores) [Note: I removed chrUn, random and hap regions from hg19 genomes]. and then use bedtools subtract to remove CpG shores overlapped with CpG island (48790) and then merge the CpG shores which are overlapped within CpG shore regions (46817 CpG shore).
Eventually, 46817 CpG shore region were obtained. and you can download this annotation: hg19.cpgshoreExt.txt
You can find the code in Perl Script for Bed file preparation for CpGI, CpG Shore, CpG shelf regions