Shape-based peak identification for ChIP-Seq |
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Authors: | Valerie Hower Steven N Evans Lior Pachter |
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Institution: | (1) Department of Mathematics, University of California, Berkeley, California, USA;(2) Department of Statistics, University of California, Berkeley, California, USA;(3) Department of Molecular and Cell Biology, University of California, Berkeley, California, USA |
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Abstract: | Background The identification of binding targets for proteins using ChIP-Seq has gained popularity as an alternative to ChIP-chip. Sequencing
can, in principle, eliminate artifacts associated with microarrays, and cheap sequencing offers the ability to sequence deeply
and obtain a comprehensive survey of binding. A number of algorithms have been developed to call "peaks" representing bound
regions from mapped reads. Most current algorithms incorporate multiple heuristics, and despite much work it remains difficult
to accurately determine individual peaks corresponding to distinct binding events. |
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Keywords: | |
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