BS-Seq on Repetitive Region

[ianchang]

Dear All,
When I practiced bisulfite sequencing mapping program (Bismark and BSSeeker) with Lister's H1 dataset (http://neomorph.salk.edu/human_methylome/data.html), I found that several repetitive regions can't be mapped (e.g. chr6:29630000-29720000). However, on Lister's AnnoJ Browser, this regions mapped well by using their approach (http://neomorph.salk.edu/human_methylome/browser.html).

Therefore, I would like to ask if anyone had this problem before? And how to fix it?

[comingme]

Several reasons I guess: 1. Mostly probably it's the property of repeats. If the aligner randomly picks one hit from thousands of mapping locations, some locations may not be given reads. 2. Different aligners treat this question differently.