Analyzing Bisulfite Sequenced Reads

Question

[sm4bhat]

Hi,

We have carried out targeted sequencing using ION TORRENT PGM of the PCR products amplified from bisulfite converted whole blood DNA. We have aligned the reads and now analysing the reads against reference sequences using BiQ Analyzer HiMod. But the problem is, can we just rely on the mean modification levels for every potential modification site of very sample for one specified amplicon generated by the software. We tried calculating the methylation percentage from the [0,1] we get from result files, however less reads per CpG site may generate higher methylation percentage. Therefore is there any way to deal with the problem. What cut off I should give for min number of reads per site?