Dramatic decrease of mapping efficiency between Bwameth and Bismark

Question

[Raphael]

Hi all,

I have mapped an rrbs sequencing with bwameth and bismark and obtained very differents results (see in the table below). I have observ with FastQC a contaminantion with illumina adapter in the samples, but after trimming the mapping efficiency decrease with bwameth. My main question is why did I observ a so important difference in mapping efficiency between bismark and bwameth, before trimming but no after trimming ? an other question: why the efficiency of bwameth mapping is so higher without trimming and decrease with trimming, it should be the opposite ?

thanks for your help

[reza.jabal]

What model organism are you using in your experiment? Human, model organism or non-model organism?