Originally posted by zhenshao
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Repetitive regions are always going to be a problem for read mapping - whether it's ChIP-Seq, RNA-Seq, or gDNA-Seq. Unless your read length (or span for paired end reads) is longer than the repeat length, there is not too much you can do. -
Does any body have any experience to identify CHIP events in repetitive regions?
We are generating a set of ChIP-seq data and are interesting in its behavior in repetitive regions. But the mapping is a problem.
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