ChIP-Cor Analysis Module

This tool reads ChIP-Seq tag positions and generates a positional correlation histogram for two genomic features. 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. The input of ChIP-Cor is a set of tag positions mapped to a reference genome produced by a ChIP-Seq experiment. We use as a working format a simplified GFF format, called SGA (Simplified Genome Annotation), which is sorted by sequence name and position. In addition to SGA, ChIP-Cor supports other input data formats such as BED, GFF, BAM, and FPS. Compressed input data in gzip or zip format is also accepted.
The output is a tag correlation histogram showing the abundance of the 'target' feature as a function of the distance from the 'reference' feature. At output, we also provide a 'feature extraction' option that includes DNA sequence extraction for selecting ChIP-enriched regions of interest.