Analyzing Bisulfite Sequenced Reads
0
0
Entering edit mode
6.1 years ago
sm4bhat • 0

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 • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 1796 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6