We had 6 samples, 3 controls and 3 tumors, for which we ordered whole bisulfite sequencing, we're interested in knowing the changes between the two control/tumor. Though the sequencing facility did by mistake a ERRBS targeted sequencing. We decided to go with it, unfortunately I've never analyzed that kind of sequences. I have access to the SAM files on our server.
- What would you do to analyze this methylation data, where to start, what to look for?
- Any recommendation of packages/software publicly available?
Any input are welcome :)