bwa settings form MeDIP-Seq

[paolo.kunder]

Dear All,

I will soon start to analyze some MeDIP-Seq data generated form an Illumina platform.
Sequences are paired end 50 x 50 bp,
I have read the following nature protocols

http://www.ncbi.nlm.nih.gov/pubmed/22402632

I have a solid background on RNA-seq data but never attempt to analyze methylome data,
In the protocol is suggested to use bwa to align reads, any suggestion on how to tune some bwa paramenters?

thanks,
Paolo