CAGT is a tool to analyze the heterogeneity and diversity of the magnitude, shape and orientation of patterns of functional genomics signal tracks (such as histone modification ChIP-seq signal) around a specific set of defined genomic anchor points (e.g. TF binding sites or TSSs)
extractSignal can rapidly extract signal data corresponding to user defined intervals from
genome-wide signal tracks (using quick random access). Several input formats are supported for the interval data as well as the signal data. A significant advantage of extractSignal is that
it is pretty fast especially when used with mat format genome-wide signal files which allow quick random access. You can also specify meta functions that operate on the signal vectors corresponding
to each interval. eg. get the maximum value of signal for each interval. You can also perform specific manipulations of the intervals themselves such as
expand or contract the intervals or automatic correction to force all intervals to be equal to the predominant interval length in the dataset.
Wiggler is the official tool used by the ENCODE consortium to generate uniformly processed genome-wide signal tracks for all ChIP-seq, DNase-seq, FAIRE-seq and MNase-seq datasets. These tracks were used in all the Sept 2012 ENCODE papers (http://nature.com/encode)