GpC Methylation

[allison4]

Thank you for this very useful tool! I have been trying to use MethylDackel to analyze data acquired from a NOMe-seq type method, in which GpC methylation (in addition to CpG methylation) is an informative mark. I was wondering if there is a way to specify only GpC contexts in the MethylDackel commands.

[dpryan79]

There isn't, maybe bismark has an option for that? I guess I could add a GpC context output otherwise, though I'd need to look at some NOMe-seq data to see if it's working right.

[allison4]

Thank you for your quick response! I looked into bismark a bit a while back and it has a NOMe-seq option. I could be mistaken, but one of the problems I encountered was that bismark does not seem compatible with BWA-Meth, which has consistently given me better alignment rates. A GpC methylation option would be very helpful, but I will keep experimenting with different parameters to see if I can improve anything!

[dpryan79]

OK, if you end up really not finding anything else then just (privately) send me a small bit of a BAM file showing a few decently covered positions. We can then iterate back and forth a bit to come up with a solution.

[allison4]

Thank you so much, I really appreciate it! I'll send you an email if I'm unable to find a solution.

[rgilsbach]

Hi Devon, are you implementing extraction of GpC methylation for NOME-seq? We are starting to do the assay in the lab. Otherwise I give Bismark a try (after years of methyldackel), if the assay works.
Have fun and relax during the last weeks at the MPI.
Ralf

[dpryan79]

@rgilsbach it was never popular enough for me to implement. I need to push out a new release of MethylDackel, so maybe possibly I can incorporate this into that...but I can't make any promises.