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  • Few Peaks

    I am analyzing a ChIP-Seq data set for another lab. The sequencing seems to have gone quite well, with a high depth of coverage (more than 4million mapped reads in each sample), with length of 50bp and Q>30. However, when I try calling peaks with QuEST2.4, I detect less than 1000 peaks in each sample. I'm trying to cover all possible explanations. Possible explanations include:

    1) Problems with ChIP enrichment

    2) problem with the control sample (but I've already tried peak calling with no input sample, and the results are the same).

    3) Unexpected peak shape/binding pattern (have tried reducing stringency, and the results are the same.

    Can anyone else think of any other explanations for this?

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