BSMap bisulfite negative strand reads

[isildur]

Dear all,



I am using the BSMAP software to analyze bisulfite amplicon sequencing data. I am trying to calculate the bisulfite conversion efficiency by using the methylation level of the non-CG cytosines of the positive strand.

Some of my libraries show very weird results in the sense that all the non-CG cytosines that are sequenced appear to be on the negative strand. This is not right since in my experiment after bisulfite treatment I amplified the DNA with bisulfite specific primers that bind only to the positive strand. Therefore only that is further sequenced.



Does anybody have any idea why I get all the reads in the negative strand and nothing at the positive (apart from CGs only)?



Thanks,