I have a question regarding calculating average methylation across all sites from one single gene. I have the raw data from chip bis sequencing in the following form.
Total reads, # of C reads, ratio
My question is since the total number of reads at different sites is different, which would be a better way to compute average methylation?
1. Take the ratio and divide by number of site?
2. Take the sum of #of C reads among all sites/ sum of Total reads?
I am leaning towards method #2 since I feel like its a more accurate depiction of the raw data but I wanna hear some opinions!