• bedtools: http://bedtools.readthedocs.io/en/latest/content/installation.html. This is a bit difficult.

To compile and install bedtools, you will need a compiler:

1. If you use Windows, use the Cygwin setup program to install 'gcc-core-6.3.0-2' (the GNU Compiler Collection; some other recent version should also be OK). In the same way, also install 'gcc-g++-6.3.0-2', 'zlib-devel-1.2.11-1', 'wget-1.19.1-2' (or some other recent version) and 'make-4.2.1-2' (or some other recent version).

2. If you use Mac, download and install Xcode (see https://developer.apple.com/xcode/downloads/). This will give you the GNU C compiler.
   Then compile and install bedtools as decribed on the bedtools website (http://bedtools.readthedocs.io/en/latest/content/installation.html).

关于bedtools使用

中文介绍参考：https://www.plob.org/article/10690.html