Analysis of ChIP-seq data.

Shown are the number of peaks called and the total number of bp covered by each peak set for H3K4me3, H3K36me3, and H3K9me3 using the original Sole-search program or the program which has been modified to identify broad regions covered by modified histones. Also shown in the increase in genome coverage (fold difference) that results when using the modified peak calling program. Both the original and the modified program can be accessed at http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi.