capC-MAP : Analysis software for Capture-C data

capC-MAP is a software tool designed to automate the processing of Capture-C data. It allows a user to run the whole analysis pipe line using a single command line. It comprises a set of C++ programs and a wrapper script written in Python. It has been designed so that the component programs can also be run in isolation for advanced usage.

Citation

A paper presenting capC-MAP has recently been accepted in the journal Bioinformatics, and is available at https://doi.org/10.1093/bioinformatics/btz480. Please cite it if you use capC-MAP in your work. A pre-print is also available: https://doi.org/10.1101/456160

Documentation

Full documentation is available at http://capc-map.readthedocs.io/

Also, a small example data set with instructions on how to run an analysis is included in the example\ directory, and a set of tutorials on how to perform downstream analysis and plotting of capC-MAP output are provided in the downstream\ directory.

Requirements

The following software must be installed on your system and visible on the path

• Python (>=2.7)
• biopython package for python
• bowtie (>=1.1.1 note that bowtie2 is a distinct piece of software and is not supported)
• samtools (>=1.3.1)
• cutadapt (>=1.11)
• a C++ compiler

Version numbers are those which have been tested, and older versions may also work.

Installation

There are several ways to install capC-MAP. One of the easiest is if the bioconda/conda packaging system is available on your system (see https://bioconda.github.io/#install-bioconda for details on how to get it). In this case capC-MAP and all of its requirements can be installed with the single command.

conda install capc-map

Some further details on conda installation are given below. If you do not have conda on your system, you will need to install the requirements listed above separately. Then install capC-MAP with the following steps:

1. Download the source code or clone from github.

2. capC-MAP consists of a set of programs written in C++ and a Python package, which both need to be installed on your system. If you have root privileges and pip is available on your system you can compile and install the software by running the following commands in the capC-MAP package directory

   ./configure
   make
   make install
   pip install .
   

   If you do not have pip installed, instead run

   ./configure
   make
   make install
   python setup.py install
   

   If you do not have root privileges, you can install a local copy of capC-MAP in your home directory using, for example, the commands

   ./configure --prefix=${HOME}/.local/
   make
   make install
   pip install --user .
   

   If you have installed capC-MAP in your home directory, you will need to ensure the binaries directory is present on the system PATH. For example, by adding the following line to your ~/.bashrc file

   export PATH=$PATH:~/.local/bin
   

Conda Installation - Troubleshooting

Version incompatibility issues for python have been found to cause problems with conda installation on some systems. To avoid this conda allows packages to be installed in isolated environments (see e.g. https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-environments). For example one can install capC-MAP in its own environment with the command

conda create -n envcapc capc-map

After installation the environment must be activated before capC-MAP is used, and can be deactivated afterwards, e.g.

conda activate envcapc

# --  run capC-MAP commands -- #

conda deactivate