Hi all,

I am doing chromatin Chip-Seq, which should in principle give a more or less homogeneous distribution of mapped reads along the genome (OK, there are small changes, which are the aim of the study, but in general all genomic regions should be populated by the mapped reads). However, for some reason I always get about 10 MB region to which no reads are aligned. I tried both no mismatches and one mismatch when analysing the data, and it's still the same. In both cases only unique matches are allowed. Is there some biology behind this, e.g. that there is a region of repetitive sequences, once per chromosome, that can not be mapped? I can see at the genome browser that this region is not a centromere, and there are even known genes in it. What could be wrong? Or may be it should be like this?

Thank you!