Hi,
I have been using CNVannotator to annotate my CNV regions and worked pretty well for me. I can retrieve a lot features from there. Only thing is for my CNV regions I found CpG sites but these sites are not annotated to corresponding gene names. I just receive the regions that match and retrieve CpG information, now I want to know to which gene these regions correspond to that got a hit in their database. I found an online tool lynx where you can provide regions in order of
chr8:12595527-43811979
chr8:183585-7808664
chr8:12595527-43926760
chr14:69961223-70005628
And then I can retrieve gene names for these regions. I would like to know if this is a right approach to annotate the CpG regions that I get for my CNV regions. The regions of CNV that matches with CpG regions in CNVannotator are returned as below. I am now taking the regions of Matched position to know the gene names of these CpG sites with Lynx. I would like some suggestions. I do not have strand information so I cannot use Ensemble or Homer. Any inputs are appreciated
# of # of Percentage Percentage Ratio of
Query position Matched position CpG in G/C of island of island observed to
island that is CpG that is G/C expected CpG
chr10:6130750-6131499 chr10:6130786-6131774 102 618 20.6 62.6 1.06
chr10:70883500-70884249 chr10:70883663-70884353 78 465 22.6 67.4 1
chr10:75910500-75911249 chr10:75910836-75911480 50 435 15.5 67.5 0.71
chr11:17410000-17757749 chr11:17756056-17758286 226 1405 20.3 63 1.02
chr11:63530500-67829499 chr11:63529888-63531834 171 1271 17.6 65.3 0.8
