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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?
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?