Unfortunately Google Group for BETA(http://cistrome.org/BETA/index.html) doesn't seem to be active, so I hope someone could help me out.
I have two datasets: - RNA-seq from Huntinton's disease and wild-type mice - ChIP-seq of H3K4me from Huntinton's disease and wild-type mice
I'd like to find an overlap between ChIP-seq and RNA-seq. According to BETA manual input files are: 1. Expression data - this is output of DE analysis of disease vs control. 2. Bed file of factor binding. I don't understand which bed file should I use though, since I have binding data for both disease and control, yet there's just one file required.
Is BETA even suitable for my analysis, and if so, what am I missing?
Best regards
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