Methylation Analysis (Bisulfite sequencing)

Question

[mks002]

Hello all,

Presently I am working on Bisulfite sequencing data for three sample, After primary Analysis using the Bismark tool. I got a bedgraph output. The output bedgraph shows position wise methylation call and the read depth.

For the further Analysis, i wanted to know what should be a better procedure for studying Differential methylation.

Would it be wise choice if we first check the methylation call at different sites ( promoter-TSS, intergenic, exon and TTS). or if would it create a wrong interpretation as the methylation calls are position wise.

Would be thankful for your kind replies.

Answer 1

[hongbo919]

Hi, we have developed a new software for de novo identification of DMRs from various BS-Seq data including WGBS. Maybe it is useful for you. http://fame.edbc.org/smart/ Best wishes! :)