is there a How to bisufite seq anaylsis page

[shawpa]

The how to/exome analysis seqwiki (http://seqanswers.com/wiki/How-to/exome_analysis) is the greatest thing in the world and I would be lost without it. Anyways, I am wondering if anyone knows if a similar manual for analyzing WGBS data. I haven't located one yet, but the internet is big place. I can't even get the most basic commands to work in Bismark (like genome preparation)! Just curious if anyone can point me in the right direction.

PS. Whomever took the time to write the exome wiki for us "dummies" is a godsend!

[fkrueger]

I can't even get the most basic commands to work in Bismark (like genome preparation)!

That's a shame, if you are struggling with anything in particular you are more than welcome to send me an email and I'll do my best to guide you through. Even though I can't offer you a comprehensive WGSBS-Seq tutorial I could still point you towards a few documents that you might find useful: the Bismark manual, a review on first steps with BS-Seq data and a brief guide to RRBS which is in part also useful for normal BS-Seq.

[Nili_Avidan]

We are using iontorent PGM for target bisufite sequence and ion-torrent software to generate the alignment and variant-call. We have successfully use this strategy for two different sets of amplicons but are having problems with the third-set that is very CpG rich.
We have try to manipulate the variant-caller parameters but are unable to get a VCF file despite the fact that we see the multiple C-T sites in IGV. Is anyone else try this crude method to get biseq with methylation percentage? Do any one has an idea what parameters in the PGM variant caller we can manipulate to get a VCF file with the data?
Nili