[daemonk]

I am working with some epigenetics data right now (chip-seq on histone modifications). The main problem I see is that there doesn't seem to be any mature framework for analyzing the data. There are a bunch of disparate methods for different aspect of the data analysis that all seem to give different results.

From the data generation perspective, there are so many possible sources of biases from preparing the biological sample to sequencing of the sample, it can be difficult to control for all these variables in the down-stream analysis.