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  • 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.

  • #2
    Originally posted by zhenshao View Post
    We are generating a set of ChIP-seq data and are interesting in its behavior in repetitive regions. But the mapping is a problem.
    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.

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