Question: Analyzing Bisulfite Sequenced Reads
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gravatar for sm4bhat
3.7 years ago by
sm4bhat0
sm4bhat0 wrote:

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? 

next-gen • 1.1k views
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