capC-MAP : Analysis of Capture-C data.

capC-MAP is a software package for the analysis of sequencing data from Capture-C experiments [Hughes2014] [Davies2016]. It is actually a suit of programs written in C++ and Python, along with a Python wrapper script which allows a full analysis pipeline to be run using a single command on Unix-based systems. capC-MAP was written so as to be as easy to use as possible, but allow maximum customisation and separate use of the component programs by advanced users. While other other tools which can analyse Capture-C data are available, these are mostly extensions to software designed with HiC data in mind. To our knowledge capC-MAP is the first software dedicated to, and optimised for Capture-C data; it is designed to be used by beginners and ‘C-method’ experts alike.

The aim of a Capture-C experiment is to obtain an interaction profile for a set of “target” genomic loci. This is similar to the aim of a 4C experiment, but the method allows multiple targets to be probes in a single experiment. This is achieved using oligo capture technology. A frequently cutting restriction enzyme is used to fragment the DNA so as to obtain interactions at high-resolution. Oligos are designed against a set of restriction enzyme fragments of interest. Throughout this manual we use the term “target” to refer to restriction enzyme fragments for which oligos have been designed, and “reporter” for fragments which are found ligated to target fragments. The term “target” is synonymous with the “viewpoint” or “bait” fragment in 4C.