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chipscore

By Vital-IT, Last update 1494698999
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chipscore description

Chipscore is a feature extraction tool for ChIP-seq data analysis. It reads a ChIP-seq data file in SGA format, and compares two features, a reference feature (feature A) and a target feature (feature B), with respect to their relative position. By default, the program extracts feature A tags that are enriched in feature B tags according to a given count output threshold or score that is 0 by default. If option -r is specified, the program extracts sites that are depleted in feature B. The feature specification must have the following format: = [<+|->] the strand specification being optional. The parameter is a name that is given to the chIP-seq tags in the SGA file. If no feature is given then all input tags are processed. The SGA input file MUST BE sorted by sequence name (or chromosome id), position, and strand. One should check the input SGA file with the following command: sort -s -c -k1,1 -k3,3n -k4,4 . In debug mode (-d), the program performs the sorting order check. The relative distance between the two features is analysed within a given range: -. A value can be optionally specified as a cut-off for the feature counts.


Parent program: chip-seq

ChIP-Seq combines chromatin immunoprecipitation with massively parallel DNA sequencing to identify the set of cis-acting targets of DNA-associated proteins or factors on a genome scale. It can be used to precisely map global binding sites for any protein of interest. Previously, ChIP-on-Chip was the most common technique used to identify trascription factor DNA interactions. Chip-Seq is also used to study epigenetic events such as histone modifications and DNA methylation.