ChIP-Extract Analysis Module

This tool is similar to ChIP-Cor in that it is used to correlate genomic tag count distributions for two genomic features ('reference', and 'target'). For each 'reference' feature, it extracts 'target' feature tags that fall into a distance range relative to the reference feature. Input features maybe ChIP-Seq tag positions, peaks found by ChIP-Peak, or any type of genome annotation data that can be mapped to a single base on the genome. We limit the size of the reference feature set to a maximum of 100'000 features. As for the orther tools, the input of ChIP-Extract is a set of tag positions in SGA format that are mapped to a reference genome. The output is a table in text format consisting of all 'reference' features (rows) with relative 'target' tag counts in bins of a given size (columns). The Web interface generates a corresponding heat map image as well as a correlation histogram showing the abundance of the 'target' feature as a function of the distance from the 'reference' feature.