capC-MAP : A Software Package for Analysis of Capture-C data

Abstract

AbstractWe present capC-MAP, a software package for the analysis of Capture-C data. Capture-C is a “many-to-all” chromosome-conformation-capture method. We summarise the method, then detail capC-MAP, the first software specifically designed and optimised for Capture-C data. capC-MAP has been developed with ease-of-use and flexibility in mind: the entire pipe-ine can be run with a single command, or the component programs can be run individually for custom data processing, in a strategy that will suit computational as well as experimental researchers. Finally, we compare and benchmark capC-MAP against another package which can perform (though is not optimised for) analysis of Capture-C data.