How does MEDIPS handle multiple mapping of a read

Hi,
I was wondering if someone can tell me what happens in MEDIPS a particular read maps to multiple locations on the genome? I have just aligned my MeDIPS-seq data using BWA and only about 40% have a mapping quality of above 30. Does MEDIPS only take into account unique reads and throws out the rest? 

I looked at the MEDIPS manual (http://www.bioconductor.org/packages/release/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf) and can't find any information on this.

I read on various forums and many people suggest just using unique reads. However, for ChIP-seq, it is suggested that one could use CSEM so that information from multiple mapping is not completely lost.

Thanks in advance for your help.

Allen



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